Conflicted Character

I have a Bajoran PC in my ICON campaign who bought Species Enemy (Cardassians) during chargen, and has played it properly for several years (both game-time and real-time). Recently I ran the PCs through the FASA adventure A Doomsday Like Any Other in which the characters must defeat a second Doomsday Machine. This one was headed for Cardassia Prime and LCdr. Seth was the one who stopped i, using his leftover Borg implants (he'd been briefly assimilated and de-Borged by the Voyager's HoloDoc, Commander Annika Hansen and Lieutenant Icheb) to fry the Machine's computer. He knew it was aimed at Cardassia and destroyed it anyway (making his saving roll against his DisAd). Now, he also has the Trait Species Friend (Cardassian) and has been awarded the Cardassian medal Hero of the Cardassian People (sorta like the old Hero of the Soviet Union). Now, he's doing a bang-up job of playing that he hates himself for doing it, but has to play nice because Starfleet is holding him up as a good example.

So. Basically if the Roleplaying is bang on, in ICON he should also be getting occasional rewards of discipline and openness renown. It may also allow the opportunity for a Kira alike arc where he finds that (as Kira did in Duet) the fact that they are Cardassians is not enough...

In a post DS9 Galaxy TBH I suspect that the Species Enemy (Cardassians) flaw is almost outdated, it may take a generation or two, but the fact that Cardassia was brought low by the Dominion, the presence of Starfleet and DS9 serving as a central lynchpin of the relief convoys rebuilding Cardassia may make this more common.

Although I dont know if this time period meets your campaign...

Should have said I could have thrown my partial Bajoran notes your way... (about 90% complete... Parenting my girls seems to take ALL the time so the final leeg is slow going...)

We did a slightly similar thing in our old TSR Marvel game: My hero (a mutant) saved a radical anti-mutant villain from a certain death against even his better judgment. I believe my position was that his commitment to protecting people was stronger than his disgust at the guy's villainy. Team mates even told me I should have let him fry.

Of course, the resolution wasn't so cheery for my hero: Every time this guy did something against mutants it was a knife in the back. Eventually the GM felt sorry for me and my character, and had Wolverine give him a little "You're a good guy, you couldn't let die, even if he did deserve it. It's why you put on that uniform." type of pep talk, and then gave me a little XP bump whenever I role played dealing with the guys actions. (Side effect was everyone trying to save badguys).

Ah, Role-playing!

Another way to look at it is Species Enemy is a disadvantage but one internal to the character, it is the character who has these feelings about the race (racism/bigotry/whatever similar type thing), while Species Friend is external and directed towards the character. While he might hate or hold a deep prejudice towards those who think highly of him, neither side can directly change the internal feelings of the other. They can influence the others internal feelings, but it is up to the character whether he wants to "pay off" the disadvantage and change how he thinks, much as O'Brien did and mentioned in "The Wounded".