I agree with the things already been said, like Jon, T'Pol and too a lesser extent Trip being out of character. Seeing T'Pol as a compassionate woman, I don't like her actions in this episode.
What bothers me most is that the Prime Directive (no interfering with alien cultures), that hasn't been writing yet, is taken to the extreme. We see in other ST series that Kirk and Picard interpretated the Prime Directive in such a way, they interfere with alien cultures when they think it's a good thing to do.
As Honeybee pointed out, when different cultures meet, those cultures get influenced by each other. That isn't always a bad thing - it also depends on how the cultures meet and how open the cultures are at that point of time. If a society really doesn't want change - change will not come, how hard the other party is promoting it.
My second point is that it isn't clear how Starfleet thinks about asylum. Are they an organization that support people who seeks freedom of thoughts and living? Judging from this episode, they aren't. However, we have seen Jon giving people sort of asylum in other episodes.
What really hurts when it comes to Cogenitor is the way Jon reacts to the suicide of Charles. People who have dealt with suicide in the circle of family and friends know that there are two reactions to suicide: why? and what could I have done to prevent this? It's hard to realize the suicide is a decision made by that person.
In the conversation between Jon and Trip Jon seems to put all the blame and guilt of the suicide of Charles on Trip, who has been the only one to show Charles that Human vitrue of kindness. I am glad Paulinem wrote such a wonderful story about Trip and Jon dealing with this situation, because I did think Jon's reaction was very bad and put the character of Jon (which I like a lot) in a very bad light.
Even when I don't agree with many things in the episode, it's still a thought provoking episode. With wonderful scenes between Trip and Charles. When I saw this episode, it was the first time I started to like Trip.