Well, I'm finding it increasingly difficult to make choices in this game.
that's exactly the point.
negative karma against the bos is only a few members i believe. the others are neutral and do not affect karma. there is a way to destroy the chapter without incurring any negative karma. but there is only one character that will tell you how. but i think you killed him anyway so...
there is also another way to solve the BOS problem.
karma is calculated per individual, not as a group. so certain members of ncr and bos will give you negative karma if you kill them, but most will not affect your karma. negative karma also does not imply that the individual's group is a 'good' group.
you most certainly can play the game and never incur negative karma. hint: sometimes people in power do things for selfish reasons, perhaps you should explore other ways of solving problems.