You should get rid of the aiptasia if you don't want it over-populating your tank.
If you rocks aren't big and moveable, I would get a cheap soldering iron ($12 In most HW stores with the thinnest tip...I like the ones by Craftsman) and spot roast the aiptasia out side of the tank... you can then rinse and put back in (though I don't bother since I burn them till it' black for good measure). Aiptasia releases spores when stressed so if you're not thorough, you'll have more down the road.
If you go this route, I would suggest using something to mark the location on the rock before taking out of water. The aiptasia deflates into a tiny gelatinous mass that's usually hard to see once out of water.
Your other opions shy of the chemical route (aiptasia-x, lemon juice, peroxide, etc) is to introduce peppermint shrimp (Atlantic variety not pacific...the latter won't do much) or a matted/bristletail/aiptasia-eating (diff names sold under) file fish. Your miles may vary here, though
. The reef version of the algae about one person's trash is another's treasure... lol.
