RE: It still bothers me
By Reklaw

I don't think Archer was just being morally whimsical. In 'Cogenitor' he objected because the cogenitor wasn't expressing disatisfaction with her circustances and Trip set about reprogramming her expectations in life. Engineering, as it were, the cegenitor's resentment of her situation, society and ultimately causing her demise.

Trip also lied and effectively invaded the alien's personal living quarters when commiting this subversion.

The case of the Suliban was completely different. Members of the Enterprise crew were victims of the same oppresive society imprisoning the Suliban. What's more, the Suliban were expressing grave disatisfaction with their circumstances. As you'll recall, even once the Prime directive is in force and mature in the 24 century, victims of warp capable societies seeking asylum or help may be granted it on the discretion of the captain. And, lets also realize that Archer is the captain on a ship with a chain of command which also gives him justification for execising his discretion in these matters - whereas Trip should not be acting independently.

On the other hand, I guess you could say that the Suliban needed winning over to the idea of revolting which is sort of different than them asking for help on their own. What's more, Archer should also be concerned about dragging Start Fleet into a war. So, yeah, he wasn't exactly being conservative or prudent in his judgment. Although he had justification because he had been unjustly imprisoned, so he was far from being the instigator.

All in all, I think there are marked differences between Archer's actions with the Suliban and Trip's with the cogenitor.