1. I think that is a terrible way to to design. Balance should be a goal from the start, not something you tack on ex post only if there is a serious problem.
2. Why would you try to push warmongers out of Rationalism? Freedom, maybe, but Rationalism? Many militaristic civilizations have been very pro-science, often arguably more so, since they're often interested in weapon development. Nazis, Soviets, cold-war USA, Japan, all pretty important technological innovators.
3. The present (pre-10.4 nerf) system has had huge problems. I have had games where I have been able to increase my science output by roughly 80% merely through declarations of friendship.