I don't like "Cogenitor" much. It tries hard to be a thought-provoking ethical-dilemma episode, but ultimately it resorts to the same lazy cheat as TNG's "Homeward": "Oh, look, one isolated individual committed suicide, therefore the Prime Directive must be right." You don't know a different individual wouldn't have reacted differently. If one suicidal person jumps out in front of a car, that doesn't mean driving cars is immoral. The suicide card is a cheap, melodramatic way to shut down debate on an issue by saying "That side leads to death so it's obviously wrong." It takes a nuanced question and reduces it to black and white. And it smacks of authorial puppeteering, the hand of god reaching in and arbitrarily deciding the question on the side the writer prefers.
I mean, what was really at issue here? Whether the cogenitors as a group, who clearly had the intelligence to participate as more than nameless house pets, could assert the right to fulfill that potential. Are we supposed to believe every cogenitor on Vissia would commit suicide if they tried to push the boundaries and were found out? Or that there was no chance that Vissian society as a whole, if challenged by the cogenitor minority to change, might actually be able to do so? Neither of those makes sense, so resolving this particular instance with a suicide is a total non sequitur, and doesn't actually say anything about the deeper issues. It's just arbitrarily stacking the deck.
See, I think one of the things that make the episode work so well is exactly that everyone seems to have different perspectives on it. To me, there was no preferred conclusion hinted at by the writing, nor were we directed to any particular perspective, which was what I so admire about the episode. I didn't see the cogenitor's suicide as a copout or a way of resolving anything; not a means to comfortably direct viewers to any particular conclusion or to draw a line of finality but a means of underscoring the whole troubling affair without offering an answer. That is, a means of keeping the whole thing implicitly an open wound rather than allowing anyone to draw "The End" under the issue. The suicide, to me, shows the depths of the potential consequences no matter what position you take or the choice you make when facing the difficult questions; questions of where you and another individual, and groupings of people in their cultures or hierarchies or whathaveyou, stand in regards to each other. It's not Trip to blame for the death of "Charles", nor Archer, nor the Vissians, but all contributed to the state of affairs that led to a person's despairing death. The contact and exchange between Humans and Vissians (and so between any societies or differing groups) had consequences, and consequences in such situations (which both Humans and Vissians eagerly embrace, we must remember!) can be serious both objectively and in terms of the self-examination they provokes. In how one evaluates their own behaviour and that of the people around them. It's the price of exploration and the price of discovery.
Is Trip right, is Archer right, was such-and-such an action or position justified? - in all, none of that matters. No matter what happened, there were going to be consequences when different cultural and moral and personal perspectives clashed, and ending in a suicide doesn't, in my book, steer us in any particular direction but merely emphasises the weight of those consequences. Unnecessary, yes, probably, but I don't see it as a copout.
Also, I wouldn't say it matters to the episode's impact what we're supposed to believe about cogenitors, nor are we really supposed to be extending Charles' situation to that of all cogenitors (although naturally we could, and that would be a natural, obvious step). The issue, as I see it, isn't about the cogenitors at all. The status of cogenitors in Vissian society isn't what the episode is dealing with - it's dealing with the question of how perspectives maco- and micro- might conflict, how an individual chooses to involve themselves or hold back from involvement with others, where they draw the line between doing what they think is right and leaving things be, whether their personal ethical biases are more important than a measured cautionary detachment. Its also an exercise in how various different views look right and look very, very wrong depending on the perspective one takes. Ironically enough (I suppose), the cogenitor as a character or as a representative of its ilk isn't, I'd claim, the point here, although naturally Charles is sympathetic as a character, since the matter of its social self-determination and worth is driving the crisis. Obviously, there's no doubt that we're being "told" that cogenitors, being as sapient as any other Vissian, should have the same freedoms, but that's obvious. The episode doesn't concern itself with What Should Be So in that regard, because it assumes that we're all in agreement there, which is no doubt true. It's everything else that's the problem.
Also, I don't agree with what seems to me to be a key argument in what you say - that "playing the suicide card" is generally (or at least on this episode specifically) a way to show a particular conclusion as inherently wrong or otherwise tip the narrative judgement toward a certain position, because another position "leads to death" (or did in this case). If suicide serves the narrative purpose of illegitimating that which led to it, then what led to this suicide wasn't one thing but several things working in concert. I didn't read the episode as claiming that "Trip shouldn't have interfered" when one can just as easily say "The Vissians shouldn't have blocked Trip's interference".
Again, as Trip says to Archer, "not your responsibility". Is it? In a sense, maybe? Yes? No? Not just mine, everyone's, no-one's? What led to Charles' suicide was the whole situation, and that situation can be summarized as "Humans and Vissians boldly go and meet each other", the exact purpose of both their missions. Does Charles' death thereby illegitimate contact, exchange and challenge between cultures? No, of course not, which is why Archer knows that he has to poke around in Pandora's box even if he knows what he's unleashing, and why even though he's angry at Commander Tucker the officer and himself as The Captain Setting An Example, he isn't angry with Trip the ethically proactive Human. That question of responsibility that Trip speaks of hangs there unanswered, just as Charles' suicide will hang there as an open wound reminding everyone of the importance and power of these dilemmas and what can be at stake.
That's how I see it, anyway.

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