Emotion and rational thought are antithetical.

Emotion can work against, or in conjunction with, rational cognitions, depending on the specific case at hand. For example, hypocrisy tends to anger people, and desire to avoid hypocrisy may lead people to avoid contradiction in their views (I say "may," because of course not everyone will even scrutinize themselves for hypocrisy, only others).

Reading about something like Lysenkoism makes me mad, but that emotion might actually inspire people to be more rational, rather than less, in considering science.

Emotions are but one of many heuristics in coming up with arguments (i.e. Reichenbach's context of discovery), which is fine as long as we have a rational justification for that argument (context of justification). If emotions are so strong that they are impinging on the context of justification, not just discovery, then I agree that there would be a problem.