"Stigma" is a bit controversial because T'Pol did willingly mindmeld, although when it became disturbing she wanted to stop. I think the writers genuinely forgot what happened in "Fusion" when they wrote this episode, but their mistake makes T'Pol look like a hypocrite or a liar.
With Yuris? I think it could be that he was risked his career to help her. I think it could be a defiant reaction to the High Command's action. Or it could be that the writers forgot what happened in Fusion (which would be very, very sad).
Cogenitor:
I liked this episode very much even though you could spot the doomed ending a mile away.
The Vissians were associated with light imagery. They're dressed in white robes. Whenever we see them, the lightening is soft and bright. The Visions are blonde and blue-eyed, evocative of western depictions of angels. The Vissian captain's fondness for Shakespeare represents Vissians' taste towards high culture--classic works as nourishment for the soul.
The Vissian's physical appearance is contrasted with their callous treatment of the co-genitor. Like Trip pointed out in his conversation with T'Pol, the Vissian engineer treat the cogenitor as if she was a disposable object or pet.
While T'Pol had a point about respecting alien culture, the counter-point to her position is that the cogenitor didn't freely chose her status in Vissian society. Is slavery acceptable just because a society condones it?
The engineer and his wife, which I intensely disliked, talked about how the cogenitor's actions impeded their chance of having a child. 'Do you know how long we've waited...' makes the debate about them and not a question about a sentient being's autonomy. For all the Vissians are associated with enlightenment, what lurks behind the surface is something darker.
I wondered if T'Pol's position would have differed if Vulcan society encouraged individualism. Vulcan society preaches the needs of the many outweigh the needs of the few. From a strictly unitarianism perspective, the cogenitor provides substantial benefit to her society if she remains in her current role. Whatever rights she has towards an individual identity is irrelevant.
Also, considering how technology advanced Vissian society is, why haven't they ever bothered researching alternative methods of conception? They could try synthesizing the enzyme that the cogenitor provides. What if a freak disease robs Vissian society of all their cogenitors? It's fool-hardy to rely on 3% of your population for your species' survival.
I thought Archer's decision was pragmatic. He spent the last two days interacting with an alien wiling to share amazing technology, and shocker of shocker they aren't asking for a pound of flesh in return. Furthermore, he bonded with the Vissian captain through their shared love of Hamlet and that near death encounter. I think one of the reasons why Archer went out to space is to explore, make those first contacts and connect with the other side. Trip's actions undermined the relationship and feeling of success Archer achieved over the last two days. It served as a professional and personal betrayal.
I thought the ending was impactful. Sometimes, good intentions aren't enough. Trip was naive. He kept thinking that Archer would be on his side. Trip's initial actions was motivated by a desire to help, but he let the genie out of the bottle. The cogenitor's suicide is not something he could predict, but in hindsight--is introducing the caged bird to the fact she's caged and going to remain caged going to end well? Trip gives the cogenitor false hope and it ends up killing her.
The show made the cogenitor's end more tragic by showing her evolution. In the beginning, she distrusted Trip. She's afraid. She wants to remain within the stratified lines of her role. Then she learns how to read. It opens a world for her. She displays delight. She acts as if she was a young child, learning these experiences for the first time. There's a sense of wonderment. When she beats Trip, it shows her potential. The metaphor of climbing mountains expands on the idea that the cogenitor's potential is limitless if not for the society she is bounded by.
The suicide can be seen as an act of defiance. It's within her control. It's something that the Vissians can't take away from her. Furthermore, the cogenitor is at a point of despair. Now that she knows she can't go back to old life (i.e. Bovary, Madame Butterfly).
I think Archer was harsher than he should have been. Trip fucked up, but it's not as if Archer hasn't committed actions in the same spirit as Trip. They just didn't entail exchange of useful technology that was in the Vissian situation. Archer's previous actions were motivated by a desire to help the impoverished. Whether or not that makes him a good leader is up to debate.
The reference to Hamlet caught my attention. In a way the episode is analogous to what happens in Hamlet. Not just because everyone dies but one person's motivations causes a change of events that neither fulfills the initiator's desires nor leaves anyone else satisfied.
It's also interesting that the episode took place next to a burning sun. It reminds me of supernovas, which the cogenitor could be analogous to. Her moment to be brilliant lasted but for brief moments before she was extinguished.