Do you plan on taking the rock out to just kill the Aiptasia?
Aiptasia are actually very effective at harvesting nutrients, they make excellent mechanical filters
I read recently read the "Book of Coral Propagation" by Anthony Calfo and there is an article about using Aiptasia just for this purpose.
I would probably just leave them in the sump.
Maybe if you are real paranoid about them spreading in the display add a UV Sterilizer on the return line, I would think that would limit their spread only to the sump
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