If they did it well people wouldn't be confused about him.
But this confusion only arises because they removed the option to kill him. He started following you, maybe out of his own will, maybe under orders, that doesn't really matter. At some point after serving you faithfully, and maybe even becoming romantically linked (Most likely real feelings) he shows his true colours once Baras asks him to betray you. And those true colours are that he feels more loyalty to Baras than to you (Not that he doesn't like you, or woudln't be loyal to you in any other circumstance, just that he feels he owes Baras more).
The options you should have had are 'kill him for his betrayal' or 'leave him alive because you now know he will show you the same loyalty that he showed to Baras". It only falls down because you lose out on the most popular choice.
I don't see that people are confused about Quinn. The threads I've seen, rather, are more emphatic, full of wishes to shock-collar Quinn, toss Quinn out an airlock, torture Quinn repeatedly, etc. Others, like me, indicate a certain fascination with him. Who is he, where did he come from, why did he do it? It's only that, as a character, Quinn seems inclined to create a rather visceral emotional response, in fact. Since story-telling is designed to create exactly that sort of response -- one that's emotionally charged, I mean -- the writers did a good job where this character is concerned.
I honestly think that without Quinn the entirety of the Warrior story would be beyond blah boring. Seriously, it would be nothing more than monotonous routine involving the killing of one enemy after another. Instead, you have this one episode that makes you stop and go, "Whoah, what the heck just happened?! Huh?" Quinn makes things interesting
, imo. That's all.
In the end, if someone gets the chance to kill Quinn, it's nothing to me, actually. I'd be losing NOTHING whether it's the most popular course, or not. Cause my warrior didn't and won't, ever, kill her captain. But that's just her. She had her reasons, as I described earlier, and it worked. To each their own.