flatworms tend to be parasitic, so yes, chances are they will munch on your coral...even if they dont, if they cover the corals they will not be able to photosynthesis = death
as far as natural consumers for a 5.5, there isn't much...in fact i can't think of anything off the top of my head which would be happy in that setup afterward other than bristleworms, and you can't usually buy those, they just happen...maybe you can get a rental from the lfs or something....sam might have an idea though which im not coming to