I've been thinking about a few issues:
1) Medicine is usually worth ~6 VPs over the course of a (3 or 4) player game.
2) It sucks to be the person who gets shorted workers early on.

So, my proposed variant: Pestilence costs you 1 VP for each city beyond three, instead of a flat 3 VP. Medicine still negates, of course.

At least now the player who gets shorted workers won't suffer (as much) if the early people start a pestilence war. I'm tempted to make pestilence affect everyone (not just opps), but that's a bigger change. (Another thought is to make only the first two cities immune, so that everyone looses one without medicine).