I remove all corals from the rock. It ends up being a complete reaquascaping nightmare-um.. I mean chore. Everything is removed save for the mushrooms. I even had to pull out the chisel to remove my favourite corals from infested rocks
I feel your pain. Oddly, even after all that effort I went and threw a rock of blue mushrooms into my new 150g tank
Surprisingly they are keeping to themselves but I have had to give away a few prunings.. that reminds me, I should prune this weekend.
The other thing you can do is just sell the darn mushroom rock. There are lots of people out there who'd be more than happy to take it off your hands I'm sure.