From memory, I think Obi-Wan got hit because he was on strange-animal back going up a vertical wall. Most of them were either mounted/driving or the only Jedi for miles.
Seriously, you can't love the KOTOR games too much if you're going to be disappointed with troops killing Jedi. You've got a line of non-Jedi parties fighting Jedi. Atton has his whole spiel about killing Jedi without the Force in II (which was one of the coolest moments in Star Wars - up there with "I just totally launched a couple hundred cloaked asteroids").