I have a hard time with it, too. In the first game, where I had to kill Mission, I just felt terrible...couldn't believe there was a Teen rating for a game where you dice up a 12-year-old girl with a lightsaber. The DS romance dialogue with Bastila was great, though.
In KOTOR 2, it doesn't really bother me to kill the Jedi - they are warriors, after all, and I have a plausible reason to oppose them. But some of the civilians...Naddaa and her daughter, Aaida and her husband...I mean, yuck, you need a long shower to wash off the slime. And I have not yet been able to kill Queen Talia...what kind of honor is there in that? Its bad enough to help Vaklu and his goons.
It seems to me the DS is about amassing power, not acting like some petty thug, butchering civilians for a few credits. You might not want to engage in acts of compassion, as that would show weakness. But being an errand boy for the likes of Visquis makes no sense - its beneath the station of a Dark Lord of the Sith. Come on now, its a matter of perspective...crushing the galaxy beneath your iron fist is the plan here.