The macro I started my fuge with had tons of these guys. I treated it right away (as it was localized to the fuge.) I think I did 3 treatments on the fuge and eradicated them. First was recommended dosage, then 2X that, then 3X recommended. 5-7 days apart on treatment. Wiped them out and never saw one again (although I have seen some big clear flatworms, which are pretty cool creatures.) Had a big mushroom in the fuge that survived fine. The 3X dosage did some damage to the pods that were in the fuge though.
So, that works if you want to nuke them with chemicals. Not sure how corals would react, as I just treated in the fuge, then totally flushed it and put in new water. I have a bottle of Flatworm Exit if you want to use it. I can drop it in the mail or something. I know melevsreef.com has a good page about treating with FWE.
Guy I got them from said he had them for many many years and never cared. They are fine as long as they aren't
1) forming mats and covering corals, where they are blocking the light.
2) multiply extensively to where they use up a trace element, then all die off at once.
You could take a passive approach and just try to syphon them out and see what happens. If not, you might get lucky with a 6 line wrasse or something.
Good luck.
Oh, if you use FWE, you will probably want to suck out as many as you can before treating to avoid toxin release. The toxin is only dangerous when they all die at once (which is what will happen when you put in FWE.)