I agree that one (and "Dear Doctor" for very similar reasons) felt like it was written strangely, as though they had an ending they intended but then didn't really support the ending naturally through the episode itself. It relies heavily on the audience already knowing and accepting the premise that the prime directive is good, and therefore everything bad that happens as a result of breaking the as-then-nonexistent prime directive is therefore narratively justified. This working backwards kind of storytelling falls particularly flat in Cogenitor where the species they're interacting with isn't pre-warp. In the episode Archer is off in the star exploring pod with the alien captain discussing Shakespeare because he'd given the aliens access to Earth's database; Trip did the exact same thing with the extra step of teaching an alien to read first. The entire premise of Starfleet is to meet new species and learn from them, which is exactly what Trip was doing. The fact that the new species also learned from Trip can hardly be taken as going against that premise.
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