IMO you should just play the romance out as quick as you want in spite of the betrayal. I guarantee if there ever was an expansion for romances in particular, Quinn will be convinced to betray you again, that or dump you because he's too insecure.
It's quite pathetic but Quinn is ultimately the victim of the whole ruse. He got played by Baras and if you kill him you get played by Baras as well. I really think the kill option should have been left in so people could feel the regret of acting before thinking.
It's like the whole Overseer Tremel thing all over again. Tremel warns us that Baras can sense who you truly are and is a master tactician.
Think about it: Those droids in the whole betrayal scenario weren't on your ship. Quinn must have sent the specifications to Baras, who rigged them to fail, which is why Quinn says "I should have known...I was painstakingly precise." He knew Baras betrayed him because his calculations would have resulted in your death. The fight was easy for this reason. Baras has no use for an emotionally compromised imperial officer, who was probably only convinced to kill you out of jealousy and anger. I can see Baras saying to Quinn: "Quinn about your assignment, things have changed for the worse and it is time to kill my former apprentice. Do I sense hesitancy? Do you have feelings for her? Do you really think a sith warrior could ever sink so low as to truly love (or care for) you? she'd be the laughing stock of the empire. She's toying with you and when she's done she will spit you out."
After all Quinn is definitely insecure enough about the relationship already (Pierce's letter about sith infidelity) and for all his great looks and superb mind he is self-loathing (Jedi Master Yonlach confirms this).
A master move by Baras: You kill Quinn and you lose a valuable crew member (you're only healer), and if you married him you get a big emotional set back as well weakening you for Baras in the future.
Truth is Quinn is not a confident person, which loses him major attraction points for my sith warrior. Basically the only reason I chose not to continue the romance...he's just not as attractive anymore. And I thought Corso Riggs was bad (meaning Corso isn't my type and no offense to anyone who likes Corso). I'm going to try the Aric Jorgan thingy...he seems more comfortable and confident with whom he is.
Quinn’s like the boyfriend who believes all the bad stuff people are saying about you and then takes it out on you ruining the relationship.
I must admit, your perspective of the incident is very interesting, generally people say he's either a traitor that was always loyal to baras and was just acting around the SW, or that he really becomes loyal to the SW and doesn't really have the ability/power to do much other than lose on purpose for the sake of the SW (sort of thing xD)...
what you said fits Baras and his disregard for his subordinates, (regardles of gender and romanc) if Baras thought Quinns betrayal would weaken the SW in any way it makes sence that he would set this up.
Even if it was just a message to say, 'you're not out of my reach'/'I know what you're up to'/'come get me'(?) (I still haven't progressed very far, so I don't know what the whole situation is)