I have a suspicion that the elements of harmony cannot be used like normal pony magic in a sense that it cannot be used to harm or destroy the "good" or the "neutral" (it only works on "bad things") and attacks the "bad" parts of a thing, much like how maggots will devour rotten flesh off of a wound without damaging the clean flesh, nor can it be used casually, it can only be used in dire emergencies such as in civilization-threatening/planet-threatening scenarios, additionally I suspect it follows this procedure for dealing with whatever it hits. If the target cannot be "cured" of "bad" or the "bad" in the target cannot be attacked, the target is then put into a stasis of some kind (banishment, stonification), as if it were acting on the assumption that the previously "bad" components in a thing may become attackable-"curable" in the future. I'm much inclined to believe this from seeing that it banished Nightmare moon to the moon on the pretense that it could not cure princess luna in that particular event (the elements stasised a incurably bad thing at the time). Turned Nightmare moon into princess luna, which is an example of it attacking the bad components of a neutral-good thing, and turning discord (a "bad guy" elemental) into stone, which is a case of the "bad" guy being put into stasis. In all of these examples, the "bad" parts of a thing were attacked/"cured" or the "bad" thing was put into stasis. But this suspicion can very easily be refuted when the next time it is used, which might be far more destructive and careless than last times it is used (much like chemical & biological weapons).
I have a feeling that this is all a euphemism for jail.