Jedi were never pacifists. Not even in the good old days of the original trilogy. Not even in the original film.

They are, after all, space samurai.

Cutting some dude's arm off isn't light side or dark side. It just is. The issue of light or dark side is all down to intentions and emotional state.

But that's not to say that the referenced games don't have major problems or that the issue doesn't get increasingly confusing the more EU you consider or anything. Personally, I find the whole concept of codified light and dark side powers increasingly part of the problem but that's really neither here nor there.