I have been thinking for some time now that Roy probably can't both be a just leader of Amestris and a known war criminal without violating his own ideals. The late turn of events in the manga seems to add to this theory, even though I think it's sad for Roy and his loyal supporters.
There is, however, another leader on "the right side" that is well known for running a tight ship. She could perhaps also find use for Roy as a close advisor, and be a satisfactory leader to Roy's allies. What do you think? Will Roy overcome this and be the leader anyway, or will someone else become the future leader? I can think of a couple of other possible rulers too ;D