so @darthmarrapologist has asked me to write my thoughts on why I think it makes perfect logical sense, storyline-wise, for the sith warrior to not kill Malavai Quinn during the vanilla story, and I aim to please.
I'm gonna try to be brief and also approach this in as neutral a way as possible, but full disclaimer I am a light side warrior player and Quinn-romancer, so that probably colours my interpretation here
But basically, short version is: it makes sense not to kill him because killing him is what Baras wants us to do. Do you really honestly think Darth Baras fully expected a non-force sensitive guy (as competent as he is) to be able to kill his extremely OP former apprentice? Maybe Quinn managed to delude himself into thinking it was possible (your milleage may vary on how much he entered that confrontation expecting to survive it), but Baras' entire thing is that he has plans and counter-plans.
So, what are the two most likely ways that Quinn's betrayal might play out, from Baras' point of view? Either Quinn succeeds and the warrior dies (smaller chance), or Quinn fails and the warrior kills him (bigger chance). Either way, both options ultimately end up benefiting Baras.
Wait, what, you may ask. How does Quinn dying benefit Baras? Well, it benefits him because at that point of the story, Quinn is almost certainly doing 90% of the work on board the Sith Warrior's ship. We know he's taken on the role of medic, pilot, strategist (three things he offers to do from the moment he begs us to let him join our crew, if I remember correctly). We also know from the letters he sends the player that he's taken it upon himself to order parts to repair and upgrade the ship. And he's the one preparing the mission briefs. He's coordinating with the military authorities. He's probably also writing all the after-mission reports, because look me in the eyes and tell me you think Pierce is properly filling his paperwork (if he does so at all).
Darth Baras allowed this guy to be assigned to our ship knowing he's a workaholic, desperate to prove his usefulness, used to (and expects to be) the only competent person around, and deeply paranoid that if he doesn't pay attention, someone will make a stupid decision that will end up getting everybody killed. He micro-manages everything, all the time. You know Baras fully expected this guy to just naturally end up doing the bulk of the work on board our ship without being asked, and you also know Vette, Pierce and Broonmark probably happily let him. As for Jeasa, she's probably focused on Jedi/Sith stuff way more than on the day-to-day functioning of the ship.
So killing Quinn, at that point of the story, where we don't have any other allies left (remember, we haven't met Vowran yet)? That's basically shooting ourselves in the foot. Baras knows that. He knows that if we kill him, we suddenly go from a threat who is part of a highly-organized team, to a threat that's just a barking dog who doesn't actually have the logistical support and know-how to achieve their ambitions, and needs to basically retrain their crew and rebuild their operation from the ground up. It would be possible, everyone on that crew is very competent and Quinn would be fully replaceable after some adjustment, but again, at that point in the story it is NOT THE TIME to hobble ourselves like that by offing him. It'd be like walking up to school the day of a presentation that's worth 90% of our grade and pushing the guy who's done most of the group project and has the only copy of the files on his laptop in front of a bus.
But Baras thinks it's a done deal, because he cannot conceive of a scenario in which a Sith Lord gets betrayed and doesn't immediately kill the offender. Which is exactly why the smart move by the Sith Warrior is to keep Quinn alive. Because we have been the one putting Baras' plans into motion before, so we know how he operates, and we can figure out when we're being baited and manipulated. I literally do not care how impulsive and dark-sided someone wants to play their Sith Warrior, at this point of the story the Warrior is NOT the bloodthirsty brute everyone thinks they are -- or, at least, not entirely. They ARE capable of managing their anger and thinking things through. The very fact the Warrior recruited Jaesa instead of killing her proves that, and it's probably one of the things that made Baras want to kill us in the first place, because it proved that we were capable of playing the power-consolidation game on some level instead of being nothing but a rabid dog that kills on command, and that made us a threat. So, yes, the character of the Sith Warrior at that point of the game, regardless of force alignment, would indeed be capable of stopping for two goddamn seconds to wonder if killing Quinn is the best way of dealing with the situation.
Furthermore, on a thematic level, the Sith Warrior has just spent the entire story watching Sith Lord after Sith Lord waste the empire's resources and even impede the progress of the war by squabbling between themselves for stupid reasons. Everybody wants to serve their own interests and become the most powerful guy around, and nobody is willing to just put their ego aside and put the interests of the empire first. But that's what Quinn does. That's what Quinn always does. Sure, he's an idiot to think that Baras is in any way better for the empire than the emperor. But he's not wrong to think the emperor is also a shit emperor that doesn't care for the empire and that things need to change. And once his own personal obligations to Baras are fulfilled (he owed the guy his life, his career, and his reputation; when asked to repay that dept, he couldn't refuse without destroying both his honour and his sense of self, which are the only things he has left) -- after that, there are no more reasons for him to not be loyal to the sith warrior anymore, because that betrayal was never personal, at the end of the day. He was just doing what he thought needed to be done, which honestly, I can respect. Compared to Pierce, at least Quinn has convictions.
He's also, of course, a cautionary tale, like all the companions are on some level. Quinn, despite his honour and his morals, is a pawn. He's a pawn who is beholden to a master and is therefore forced to do things he probably would never have done on his own. And isn't the Warrior exactly that, too? We're Baras' pawn, and then we're the emperor's pawn, and neither of these are good masters who have our best interests at heart. And we are consistently asked to do some fucked up shit on behalf of these masters, with no way to say no. Isn't it nice that at the end of the day, we can look down at another pawn who has just finally finished repaying his obligations and we can say "hey, I get it. I get why you had to do that. Now you get to choose who you actually want to be loyal to. And I will let you do that. Come back to the ship, and I will be the only person who has ever given you the option to choose."
Or, you know, you can just enforce his cooperation I guess ¯\_(ツ)_/¯ I don't really think the dark side options are thematically interesting but ymmv