i had the brown hydrioids, given to me from my lfs.....anyway, they were really SLOW growers but after a time they did start to spread. i would take the rock out and scrub and scrub for them only to come back. how i got rid of mine was really by accident....i had the rock in my 75g and had taken all the rock out b/c i was totally redoing my tank. i had filled all my rocks in 4 of those 5g buckets. i had the rocks in there, with no lights on them, no thermometer, no air pump....nothing for a good three days (only b/c it took me three days to re-do the tank). anyway, i put the rocks back in & one year later haven't seen them back. the lack of air flow/light/movement/temp killed them off. lucky me!
really, though, if i were to get them again i would just take out the rock they were on and do the exact same thing. no need to take all rocks out just the rocks the hydroids are on.