Hi there,
No it is very unlikely you will create too much water disturbation for the fish. Remember in the wild their breed are used to massive currents, lapping waves etc... Water circulation is the key to a healthy marine aquarium.
Is it possible to get two powerheads on the sides of the aquarium? I have three on the back of my tank more or less at same level (due to rocks impeding them) and one either end of the aquarium, not to mention skimmer and cannister filter outlet.
Regardless of the coral, water movement has to be ace. You just have to find a place in the tank that it likes, do a search in the reef forum for the particular coral and you will find something to help in there. Usually its just hit and miss with some educated guesswork.
Tim.