Ive used FE a couple times in established systems, one of them fairly large and very heavily stocked.  Some of the corals slimed up a bit, but as long as you get as close to all of the dead flatworms out of there after you dose, you should be OK.  The dead worms are much more toxic than the FE is.  Run heavy carbon and skimming... be ready to do a water change too.
Remember though... those scooters will starve to death if you erradicate the worms (in all likelihood, they are going to starve to death anyhow unless you have a large mature system), so you will need to figure out something for them.