I've never tried it, but in a tank that is set up and running that developed an aiptasia problem, I sure would. But since I had mine all torn down, I could inspect each rock closely. Every rock that had any went into a 5g tank I had set up and got treated. I used Aiptasia-X until I had used up what I had leftover (an old supply). Then I mixed up a new batch using kalkwasser to make a seriously thick paste. It worked GREAT. It was like pouring underwater concrete on the aiptasia. And because the rockscape isn't permanent yet, I could flip over rocks so the aiptasia was on the top surface making it easy to treat.
I have used kalkwasser paste before also, but usually end up clogging up my syringes or squirting it all over good stuff by accident! You are definitely better off since yours is torn down. On my 90 reboot, I'm trying SO hard not to deal with nasties like aiptasia in the first place, but you just never know when something like that is going to creep in. I'm getting my first batch of corals this week, where I will scrub the plugs and then dip the frags. We'll see! Sounds like you're on the right track with the aiptasia. Good luck!