From the standpoint of a female player on the Empire's side, I have to admit that there are moments when I twitch in regards to certain happenings throughout the story progression. I think that such a reaction is only natural, although I don't often get to see or experience any sexual violence, neither inflicted on my character nor being inflicted on others (I believe that's something male characters get to experience more), since it is after all the Dark Side we're talking about here. Slavery, genocide and the rest of what the OP describes go by just like in a movie. They stir something inside without them really affecting me.
I find it in no way exaggerated or over the top, even more so if one considers the atrocities that actually occured in the real world in times of war. Humanity's real history involves more than enough examples of such, without even having an obviously "evil" side in most cases. So how or why does this shock so much when it happens in a game and when one of the sides bases almost its entire structure on principals such as 'survival of the fittest', 'eat or be eaten' and similar?
Keep in mind that there's always the other side for the weak hearted. Unless of course the OP is referring to "when you dance with the devil, the devil won't change; he's changing you", meaning that someone might come out as a much more evil person after playing an imperial character....which I also find far stretched.