I agree with the others - baytril doesn't treat syphillis and the well accepted and very effective bunny treatment for syphillis is penicillin injections. Personally I would look around for another vet as if your vet doesn't know that and isn't confident at prescribing 'off licence' drugs, I would worry about their general ability with bunnies.
I do hope you manage to get her sorted - maybe try some ringing around or ask on here to see if you can find another practice which is more competent with bunnies...and then ask them for a refund as they've prescribed you a treatment for syphillis which doesn't treat syphillis!
But once it's been treated and cleared up, I don't see any reason why he can't be neutered as normal and then bonded. Make sure you disinfect everywhere really thoroughly just in case any of the syphillis organisms are still around his house, just to make sure he doesn't manage to reinfect himself once he's being treated.