Okay allow me to dig into this and post this LONG analysis I've made.
The game definitely provides moral ambiguity just not in a "the antagonists are actually the good guys" way but more a muddy conflict
The point is that while Joseph isnt a good guy the deputy isnt tackling the situation correctly in any way neither both logically, morally and not least lawfully.
In the game deputy takes things very much beyond "doing their job and duty". Throughout the game the deputy does and partakes in a lot of things morally, logically and lawfully wrong storywise considering who they actually are and what they are supposed to do regardless of the nukes or if Joseph wasn't right about the collapse and yes a lot things can also be considered unnecessarily violence... In that subject there is plenty of moral ambiguity to how the deputy does things especially as a so called officer of the law in which they completely break the law many many times.
So im gonna drop a long post explaining this:
Firstly the deputy is not exactly wrong because they are trying to stop a suspected criminal cult leader at first hand but more the way the deputy goes on about the situation post the tutorial AS IT IS SET UP which is wrong... It is more about how the deputy goes on about the situation and decides to directly wage war against Edens Gate the way they do instead of more doing what's correct and prefer to do things in a less violent manner which is why the secret ending is ultimately the right thing to do which is the whole point. And no that doesn't mean ignoring and leaving Joseph for good but simply that you leave to inform the outside world and plan a better approach with more reinforcements to even possibly force a surrendering which leads to less casualties on both sides which should always be preferred and the right thing.
Like Joseph tackle his "preparing for the collapse" wrong the deputy tackle the situation wrong aswell and does a lot of things morally, logically and lawfully wrong in the course of the game.
- The deputy never acts like a police officer and never do arrests even when possible and many things we do is completely illegal aswell.
Many of the missions we take part in or things we do in the game is either morally or logically wrong aswell as a police officer and supposed good person...
- The deputy takes part in a mission killing cows with fire and reapers because he needs the testicles for an annual festival - very necessary in the situation i see. ;)
- The deputy teams up with actual criminals from the resistance and flames angels(actual people) without remorse while freaking out to disco music.
- Chasing a dude and purposely shoots him lethally and canonically picks up his body to unnecessarily throw it around - unnecessary brutalism and wrath is not a good guy at all...
- Takes part in "voter suppression" at a street corner and literally kills people just for fun and again indiscriminately murder a lot indoctrinated people who are brainwashed or tortured into it aswell or people who only are with Joseph to stay alive or to be saved. (Definitely not only self defense neither)
- Blows up a lot of useful buildings(hotels and water treatment plant) and things which could have been reformed and used aswell.
- Blows up a statue and burns a book at the top. (so professional)
- We are actively seeking to kill people and builds up a resistance and takes part in anarchist resistance missions as a militia guerilla fighter and storywise it is not like we only kill people in self defense as we are the one on the offensive leading a resistance and seeks to kill.
- The deputy actively feeds a war and never attempts to do anything else which leads to a lot of casualties and destruction on both sides.
- Ahh and all the casual stuff: Steals and pillage stuff from local business and personal property's, indiscriminately kills animals in various brutal ways, steals vehicles etc.
- The ambiguity also lies in the fact that many of the people in the cult are equally brainwashed or tortured into this aswell and could be redeemed but the deputy never shows interest in such options or acts like an officer of the law even when possible.
Faith is a good major example to that and a person who possibly could be helped and that we as the deputy murder a young(almost barely an adult) victimized/brainwashed girl who literally breaks down and begs for help/mercy and in the end tries to reach out and basically surrender but the deputy doesn't show any desire to help her, directly rejects her and leaves her to drown/bleed out in a river - what a hero! Killing a clearly mislead young girl screaming for help should definitely cause some moral conflict and it should be the preferred option for ANY good person or anyone with any morals to help someone like her out of this by all means let alone your duty as an officer of the law.
ANY good person should be able to understand that people may be caught up on the "wrong" path doing bad things and thus by all means should attempt to help the person and prefer non lethal options EVEN if the person is responsible for bad stuff and even more if the person is like her, still very young and clearly clearly victimized in this herself to a great extent and shows a lot of inner struggle and redeeming qualities directly starting to scream and beg for help.
She is textbook definition of the objective moral ambiguity factor: "having the player killing tragic or mislead people caught up in a bad situation" So if the player doesn't see any "moral conflict" by literally killing a young brainwashed girl crying for help like her lost in this herself who does the only thing she knows and has ever learned or see why you as an officer of the law and supposed good guy should react to that, then it is definitely a problem with your moral compass and immorality rather than the game failing to present ambiguity or moral complications... Not only is it directly our job and duty as an officer of the law to step in and react to/help someone like her finally breaking down begging for mercy but also just any person with healthy morals would see a moral obligation to do so - nothing moral, good or right about murdering an almost barely an adult girl begging and crying for mercy regardless.
- Maybe the most important blowing up some well supplied bunkers for instead of just securing and keeping such very useful undergrund places intact... When we venture through them we can see that they are stocked with food, water and supplies and all kinds of useful stuff, a lot of it taken from the said county and instead of keeping the bunkers intact working to fetch all of these things back out again when possible we just blow it all up for no reason. Why care if the peggies are stealing it to prepare for the collapse if we and the resistance doesn't care about blowing it all up in the end anyway... Also by doing so you buries and smothers a lot of people (death or alive) including eventual prisoners who didn't got discovered or rescued...
Ultimately they would have been a great factor in saving and helping a lot of people in the end both in terms of food, water and recourses they now hold but also just the big space to surely hold a lot of people... The point is that a collapse is coming and Joseph build BIG bunkers. (far bigger and better supplied than the normal Hope bunkers) You rendered everything uninhabitable and made
So yeah ultimately by blowing them up you makes everything worse and possibly destroys the chance of survival for at least dozens of people, and no matter if Joseph was right or not there is absolutely no reason to blow them and it is just stupid and illogical all around no matter how you look at it but especially with the collapse coming it shows that you makes everything worse by destroying them. Regardless of Joseph and the cults horrific crimes: they build big bunkers and we made them uninhabitable and thus made everything worse. The small Hope County bunkers isnt nearly on this same svale.
They are not really "good guys", and a lot of them are portrayed as "gun-nuts" and sounds like people who enjoys this shit rather than people trying to stay alive. Furthermore you can encounter several instances in bunkers and read notes where the resistance either torture or have tortured peggies aswell and other things.
At the wolf den Tammy has captured a chosen and joyfully utilize torture on him to get information and the game makes it clear she ENJOYS it - pretty hypocritical to me and greatly adds to ambiguity and a truly good faction shouldn't utilize torture...
They burn their enemies with fire arrows and flamethrowers aswell and most of them based on comments and taunts are clearly portrayed as people who enjoys it - Jess is a prime example and she clearly takes joyment in what she does and uses the situation as an excuse to kill for fun as she basically says.
Also Sharky have his own "playground" where he joyfully flames angels (actual people) while listening to disco music - i have a hard time believing this is what a sane person would do in such situation. ;) The deputy likewise takes part in this for that matter and does a lot of stuff which a police officer shouldn't do.
I dont think they are portayed "good" and they could easily have portrayed many of them far more benevolent but this clearly wasn't the intention to show ambiguity. Many from the resistance act like people who enjoys this shit and are made in a really "fuck yeah" way rather than people who actually despise this life... The whole thing is just that one has to have some self indsight and actually pay attention to all these things yourself rather than watching a single cutscene at the end of the game like in far cry 4.
- So in the end you want to do the right thing and actually tackle things correctly? The secret ending and leaving at the start is definitely the most logical thing to do in the current situation as we are 5 people sorrounded by a army of cultists - of course they won't let you take their leader. The best thing to do is to leave the area, plan a better approach and then come back with more reinforcements as we don't really got the upper hand, so the secret ending is the "good" ending and obviously the most sane thing to do.
This would also force a more peaceful surrendering etc. And things would happen with far less casualties. This is the ultimate point of the whole thing and it should be pretty obvious for anyone having a bit of self awareness to their own character.
- Ultimately the game makes a commentary on and "mocks" this whole fps genre and specifically the typical fps audience playing it acting like killing hungry lunatics firmly believing they have "such a moral highground" and is justified to act like psychos against people they deem "bad guys" and basically that everything they do is justified in the name of being on the "side of good". The game mocks and makes satire of this whole this whole american "keep your rifle by your side" mentality potraying most of the resistance very stereotypically like these gun tooting american rednecks most of them not very intelligent who just wants to "drink beer ane shoot peggies oh yeah" taking pride in having a gun and "PrOtEcTiNg YoUr HoMe" instead of acting more naturally to the situation they are in which they shouldnt be satisfying or funny...