Care to cite an episode where a Federation vessel takes out the surface of a planet? :P
Just as Federation ships carry enough firepower to scorch the surface of a planet (stated in dialogue), a shuttle hitting a planet at many times the speed of light is going to mess up a planet if it hit. Simple physics there.
Just the fact that we're dealing with ships that move faster than light speed will necessitate standard weaponry (even defensive) much higher than what we today deem as military only.