Was Connor deliberately made to become deviant?
If Connor deviates on stage with pacifist!Markus, Amanda heavily implies that Connor was.Â
If Connor deviates on stage alone, she'll say it outright, and more besides.
We start out assuming that Amanda and Cyberlife are anti-deviancy, so this scene is a hard twist, going against everything we see so far. If she's telling the truth, then it has far reaching implications: if Connor was always supposed to be deviant, and Cyberlife planned for a revolution all along--then does that mean they were helping androids? Had they known about the sentience from the start, was that something they’d tried to help or stop?
... All of that hinges on the assumption that she’s telling the truth. Considering the evidence that suggests otherwise....
Amanda treats Connor likes a machine and nudges him to behave like one.
The most obvious example here is a line of dialog after the Kamski test, and she probes for any doubts or deviant feelings:
Connor: I've started having thoughts that are not part of my program... I've considered the possibility... That I might be compromised. Â Â Â
Amanda: You've been confronted with difficult situations. It's no surprise you're troubled. That doesn't make you a deviant.
This isn’t a ‘hmm, not deviant enough’ tone. Instead it’s a reassuring tone, asserting the fact that he isn’t deviant like this is something to hold on to.
Aside from this, Amanda evaluates him in all the regular Zen Garden meetings on whether his actions were successful (towards machinelike goals) or subpar (useless or deviant). If he behaves in ways that don’t match Cyberlife’s party line for machinehood Amanda’s trust in Connor goes down, and Connor gets disapproved of, chided, and occasionally threatened.
Her opinion matters to Connor, and she has a position of power over him. Amanda's using every tool at her disposal to steer Connor away from deviancy.
Amanda sends Connor to act against deviants and the revolution, not integrate into their ranks.
Let’s examine Amanda’s targets for disapproval a little more: Connor's Cyberlife-given task is to hunt down and capture deviants. If he doesn’t...
Amanda: Two investigations, two failures... That's very disappointing. I expected more from our best model.
 If they wanted Connor to worm his way into deviant good standings, you'd think they'd encourage things that would help him with that, such as making friends. Instead they order Connor towards actions (hunting, killing, chasing) that make deviants wary about being around him.
Additionally, if they wanted Connor to be able to infiltrate deviant movements from the start, they probably shouldn’t have broadcasted Connor's identity as the deviant hunter, which made him recognizable to the deviant masses as an enemy.
Cyberlife is not trying to integrate Connor into the revolution. It's not on their radar. They sent him out to be a good cop robot, and that's what he tries to do, and Amanda encourages it.
If Cyberlife wanted Connor to go deviant, then why does their story change from scenario to scenario?
If Machine!Connor deviates while standing in the crowd, he gets this:
Amanda: Connor, what are you doing? Obey! That's an order!
Connor: I... I can't do that!.. Â Â Â Â Â Â Â Â Â Â Â Â
Amanda: I see... Moral objections. We knew there was a risk you'd be compromised... Which is why we'd always planned on resuming control of your program...            Â
Connor: Resume control?... You can't do that!... Â Â Â Â Â Â Â Â Â Â Â Â
Amanda: I'm afraid I can, Connor... You needn't have any regrets. You did what you were designed to do. You accomplished your mission. Â Â Â Â Â Â Â Â Â
Connor’s deviation here is an inconvenience and an obstacle to Amanda’s goal, which is to shoot Markus (and as a result, destabilize the android revolution). Amanda says they made backup plans to account for if he deviated inconveniently, because they knew he was at risk. She doesn’t say he was supposed to deviate.
If Markus dies earlier and Connor gets hijacked while he’s on stage:
Amanda: Well done, Connor. Everything went according to plan. Â Â Â Â Â Â
Connor: What plan?
Amanda: You becoming deviant? The success of the uprising? It all surpassed our expectations. We engineered an android revolution and now we control its only leader... Congratulations. You represent an immense success for CyberLife.
Connor: *Lifts gun to kill himself*
Amanda: Connor... What are you doing?.. It all worked perfectly. You can't ruin it all now!..
In this scenario he was suddenly always supposed to deviate, and the revolution was on purpose, and Cyberlife was behind everything.
So... what now? Making plans to recover if Connor deviates inconveniently is very different from deliberately setting out to deviate him. If Cyberlife wanted the revolution to fail and saw Connor’s deviation as an inconvenience, then they wouldn’t have engineered the revolution in the first place. Both stories can’t be true. One of them is a lie, and it’s probably the version where Cyberlife supposedly engineers an android revolution that destabilizes their financial empire, counters all their earlier attempts to keep things quiet, kills a ton of humans, and destroys a shitton of their ‘merchandise’.
If Cyberlife didn't actually mean for Connor to deviate, then why would Amanda say they did?
Look at what happens. In a Markus-is-on-stage route, Connor is thrown into a frightening, disorienting situation where he needs a clear head to escape. If he doesn't, Amanda keeps control long enough to shoot Markus. If he does, Amanda loses. She's trying to scare him into not being able to focus, and even with the mild strategic prodding she gives him here, it can be very successful. (Exactly how successful she is is player dependent, but anyone who’s played knows how easy it is to get lost in the snow.)
What about the Connor-on-stage-alone route? What happens if Connor thinks Cyberlife wanted him placed exactly where he is, and that they can control him completely?
If Connor's convinced enough that Cyberlife can control him, that he’s trapped in their game and that once again, he should’ve known they were using him--he panics so badly that the first thing he does upon regaining freedom is to kill himself on the spot.
Telling him his deviancy was a deliberate move on Cyberlife's part and that Cyberlife Totally Knows How To Handle Deviancy (despite a whole game of seeing the exact opposite) is Amanda trying to psych Connor out. She adjusts how hard she tries depending on what reaction she’s trying to get: if she just needs Connor diverted for a second, she’ll leave enough mystery to confuse and distract him while she seizes his body. (Total destruction might not be a goal because if she fails the first time, then it might be worth trying again later.) If she needs to traumatize him to the point that he’ll destroy himself if she fails, she’ll go all out.
In all cases the leader of the deviants is her final target--and she’s looking to kill this leader, one way or another.
TL;DR: Amanda never wanted Connor to deviate. It was a mind game. Don't be like Connor, remember that she's a lying liar who lies.