Why not? How does adding factual knowledge get rid of people's desire to hurt someone else out of revenge?

Learning about the game-theoretic roots of a desire seems to generally weaken its force, and makes it apparent that one has a choice about whether or not to retain it. I don't know what fraction of people would choose in such a state not to be vengeful, though. (Related: 'hot' and 'cold' motivational states. CEV seems to naturally privilege cold states, which should tend to reduce vengefulness, though I'm not completely sure this is the right thing to do rather than something like a negotiation between hot and cold subselves.)

What it's like to be hurt is also factual knowledge, and seems like it might be extremely motivating towards empathy generally.

People who currently believe in superstitious belief system X would lose the factual falsehoods that X entailed. But most superstitious belief systems have evaluative aspects too, for example, the widespread religious belief that all nonbelievers "ought" to go to hell.

Why do you think it likely that people would retain that evaluative judgment upon losing the closely coupled beliefs? Far more plausibly, they could retain the general desire to punish violations of conservative social norms, but see above.