If you can isolate the rock like you have, then I would try to kill the aiptasia with chemical means. ( Kalkwasser, Vineager, lime juice, etc.)
I see peppermint shrimp as a control method.
Best to eradicated aiptasias if you can.
You should never boil live rock or coral, as they say that the corals could leach out deadly chemicals, especially the zoas and palys.
If you don't mind killing everything in your rock, than you can ..
Let it dry out and leave it dry for a week or so..
Soak in Bleach ... but then you will have to rinse and air dry to get the bleach out.
Soak in hydrogen peroxide...
Do some forum searches for the proper amounts to use per gallons for both above, and how to prepare the rock afterwards before putting in the tank.
Once you've killed the rock, putting it back in might cause an ammonia spike based on how much you killed in the rock and it's size and how much other filtration you have in the tank.
To rid the rock of some of the dead organics before putting it back in the tank you can cycle the rock on it's own.
You can cycle rock for a few months in the dark (called 'cooking' the rock) which is probably overkill in our case.
Or some people soak the rock in vinegar or a mild acid over night.\
Again, do some forum searches on how to treat rocks to get rid of dead organics.
