This might sound stupid, But I could see killing 5 or 6 large guys at once with no ill side effects, but If you go in there and go on a killing spree arn't you going to have Nitrates through the roof once all these start to rot?
I guess the way I see it is there is no way you can kill a small enough number without poisining your tank and still over come the amount that you have. I think they will spread faster then you can kill them safely.
It may be time for drastic messures if you want to eradicate them. and save the rock, I have "Cooked" my live rock to get rid of Bryopsis alage and it worked great. My tank has never looked beter, and there is no sign of alage in my tank. it has been about 6 months since I cooked them.
For some of you that may think I mean actulay cooking them. l(like in a oven) I'm not, and that would be nuts. I am refering to removing the rock and putting it in a large container of saltwater and covering it from light.
you then have to do ALOT of saltwater changes and swiching of the rocks. I did it once on Sundays and once on wensdays for about 2 MONTHS!
This method will cause the rock to eat itself as there is no light and you a doing 100% water changes. (you dont need the saltwater to be at 1.025 SG lower SG will keep the Bacteria alive as well)You will lose any Coralline alage and any Visable signs of life on the rock Including your little buddies. BUT the rock will still be VERY alive. all I did was put in a few new pices of LR and you can't even tell my rock was out of the tank now.
That's just my thoughts. any way you go be ready to make LOTS of water.