Re: Obvious plot hole at the beginning
The question really is, if it is moral to not intervene when the harm done to the culture is complete annihilation.
I believe that given the opportunity, the Federation Council can and would vote an exception for such cases. The problem is that such cases frequently come in locations and circumstances where it isn't practical to let the decision be made that way with the delay involved. So Starfleet - at least the Starfleet of TOS (TNG and beyond seemed to vary depending on the writer) - has what seems to me to be a very reasonable way of handling things: if a man or woman of intelligence and good character, (hopefully) such as those that would be placed in command of a starship, decides that the situation is worth their career to take the chance to save people, then the unwritten rule is that they can do that, and then Starfleet and the Council can decide whether or not they were right, after the fact.
As the brilliant philosopher once said... Everybody, have fun tonight. Everybody, Wang Chung tonight.