My friend, with all due respect, I wouldn't kill them. There are numerous methods to remove them based upon size, size of the rock they are attached to, where they are attached, location of rock, (be it a foundational rock supporting the reef or otherwise).
Personally I wouldn't try scraping them either, which in and of itself could cause the mortality I'd hope you'll avoid. Also, though many will publically state the scraping/manual removal of palythoas underwater is safe, there is well and lenghty published literature which states the documented proof that PLTX does indeed exist in a small numbers of palythoas. Not to cause you any alarm, but the scraping of palythoas under water and possibly having a minute cut in your cuticle, could cause some possible issues even if PLTX isn't present. Though far fetch, it's possible.
If you could provide a macro picture or details on where the Palythoas are relative to the SPS colony, number of polyps etc., I'd be glad to help you.
Is it feasible to move the SPS colony?
Good luck
MUCHO REEF