I still don't remember anything from it. Perhaps I'll watch it later or tomorrow. But from what little I gather from the thread, Phlox acted correctly.
The whole point of non interference is meant to ensure Starfleet's footprint on the galaxy is as small as possible and that any involvement or action maintain transparency. In other words, treat everyone and anything as if you were never there in the first place. It's like when you go camping and the ranger tells you to leave your site exactly the way you found it.
The problem is, people confuse enlightenment with morality and justice. They are not the same. Phlox's actions May not have been moral. They may not have even been just. But they were enlightened.
To play devil's advocate let me pose this hypothetical:
Say it's 1519 and some Vulcan scientist is in the Sol system doing a survey. He starts having engine trouble and has to land. He ends up smack dab in the middle of Tenochtitlan.
It's right after La Noche Triste and Montezuma has just won his decisive battle and Cortez is retreating. However, the first bodies have already started falling and Smallpox has infected a good portion of the city's population.
Back in his shuttle, the Vulcan has enough hypos to inoculate the entire city and surrounding tribes. Does he do it? Does he have the right to, and if so, should he be obligated?
Remember, if it wasn't for the smallpox, Montezuma probably would have chased after Cortez and annihilated his army--or at least decimated it to the point they had not other option but to retreat back to Spain.
In the meantime, all those surrounding tribes who had long hated the Aztec had started to realize they had a grave common enemy. In the months it would have taken more Spanish armies to return, they could have allied. This would have had massive implications on the long-term evolution and progress of Western culture.
Of course, the Vulcan doesn't know any of this. All he has is his logic and what he sees in front of him.
What does he do?