They do indeed pay in bitcoins. The payment transactions during the fork weren't lost, however-- they were confirmed on both branches of the chain. The only transactions that disappeared were the block reward transactions on 0.8.

If pools paid miners using bitcoins from their own mined blocks, this problem would go away-- that's not a bad idea!

edit: I asked -- some pool operators apparently already do this. The ones that lost out are the ones that don't.