Kirk having the power to glaze a planet without restrictions is maddening. You know, one can not launch nukes unless two people turn their keys at the same time... I remember Scottie was on board about glazing the planet like they have done it once before. No one on the bridge battered an eye about the order... It seems SF captains level planets at will...
"A Taste of Armageddon" , Kirk completely upends these two planets society because Kirk believes war should be hard and dirty. He was playing God. His moral righteousness is better than those two societies moral compass... He has the power of a God to force his will upon these two societies with his righteous judgement, like God in the Bible did to Sodom and Gomorrah...
I would hardly call it 'without restrictions'.
SF doesn't just casually go around blowing up planets for one thing (in fact, they go through incredible lengths to save them for the most part, when its allowed - at least most of the time - some morally ambiguous situations however have been witnessed, but on the whole there were extremely few).
We also have no evidence that Starfleet EVER actually went to such lenghts in practice (blowing up a planet).
Sure, Kirk may have mentioned he could level the entire planet, but he never went through with it.
There is a difference between using a potential scare tactic to prevent a threat, and actually doing something on a practical level that approaches that magnitude.
SF captains can use potential scare tactics into avoiding a catastrophic outcome, and lethal force is on the very bottom of that list (in fact, except in times of war - and even then there will be exceptions - lethal force is AVOIDED like a plague).
But when have we actually seen them implement scare tactics in diplomacy/talks?
It's usually with species or individuals that are more militarilistically minded and responded very poorly to diplomacy... in fact, I don't think it occurred more than a handful of times.
What do we know though?
We know that UFP starships can incur massive damage on not just a planet, but also throuhout the galaxy (by using subspace technology)... so, from this perspective, you can say that SF is out there 'playing god' (ridiculous term btw since religion is utterly preposterous in general if you ask me) every time a decision is made to explore.
With ever advancing technology and science, species and their ships abilities increase in magnitude greatly... so the scope changes.
The only way people could possibly see a 'way out' of this conunndrum would be that SF does nothing at all and stops exploring completely.... but then, we wouldn't really have Star Trek, would we?
To say nothing of the other species who have established massive interstellar organisations spanning thousands of lightyears (they actually WENT through great lengths to destroy planets). Starfleet only mentioned they COULD do it (a handful of times no less) as a detterrant.
I wonder if you might be casting the blame on the wrong fictional characters.