Klaus originally was supposed to be much more evil than he turned out to be. I am sure that Klaus put a "remove copy app" in Gil's head that can be triggered safely. It could be automatic when certain events occur, namely when the real one is free. While Klaus fights very hard for the Empire, if it came down to choice of Empire or Gil, the Empire will loose every time.
Do we know that for certain?
Klaus does do a lot of things you could call evil. But unfortunately they also just sadly seems to be justified in a lot of cases.
(for most sparks, brain coring Other is a logical decision)