It depends what's in your mind and heart when you choose.
The premises and storylines, lately in games, are so reduculous it's hard to take too seriously. Honestly, though, everything ha some kind of overtone be it political, socio economic, religious, or anything of the sort. I no longer look at it in a simplistic way because whoever produced that may have been trying to ingrain their ideology and mind into it in order to implant that into the consumers of this media. I don't need to be told what to think or how. I don't need anyone's over-simplicity or over-complication.
I never got any "communism" leanings from Super Mario Brothers but I did see a video giving a convincing argument that Mario and Luigi may in fact not have been italians at all but rather Comrades. Not really sure I completely believe it.
So when you ask me about feeling bad about being bad in a game...the only time I ever might is if it wasn't contrived, wasn't needlessly complicated, just realistic and straightforward. Believable. It usually isn't.
No. Not usually.
This is what I have a problem with in SWTOR--too few options to choose and no "all the above" where sometimes it would work best. I have no problem offing someone whom I believe is "too dangerous to be left alive". "Good intentions mean nothing if a greater harm is caused".
I think I can discriminate and call it if I see a difference but I do have to be careful I'm not playing god and passing judgement.