The clownfish will probably kill the goniopora. They are very sensitive to other critters touching them and usually retract. However, if the goniopora isn't retracting, I don't think there is a problem.
Make sure you research goniopora/flowerpots corals. They are a VERY demanding coral and most people have no luck at all with them. My advice is that you dose phyto pretty liberally 3 times a week and feed them VERY finely chopped, meaty foods. If you can chop the meaty food another time, then it is too big.