Everything you say is WHY this is one of the series greatest episodes. Because it's full of issues and challenges us on the very Trek assumptions of non-interference. We've had the prime directive and respect for other ways of doing things shoved up our noses since forever and it's good, very very good to see what this can actually mean for individuals and cultures. In this case both suffered from interference and yet we can't bring ourselves to not sympathize with the interference.
I like seeing how incredibly complicated inter species contact really is, not just silly things like the Tak Tak
but the real horrors and dilemmas of completely different cultures and physiologies and people. Too often in Trek the Feds save the day through pious speeches, or they walk away and pat themselves on the back for doing so, either way everyone wins. This time no one won. No one. And that was just a whole lot more interesting.
And that's where the "plus" comes from. My problem with this episode wasn't the fact that it dealt with a difficult dilemma, or that non-interference was challenged (at least by Trip). My problem was that out of ALL of the senior staff, Trip was the ONLY one to see a problem with this species. Even Archer and Co. immediately considered, and even tried, helping that colony of people that held the developing group back, all the way up to actually creating a cure. And there, the developing group was treated A LOT BETTER than these Cogenitors. I strongly feel that instead of leaping off to go joyriding as soon as he meets these people, as the Captain of the Starship, Archer should have taken a little more care to get to know them a bit. If that meant he didn't get to have some fun with their leader in the end, then so be it.
Their mission is to explore and get to know about the new civilizations they meet, and that has to come before fun. I don't even know if he stuck around long enough to know that a Cogenitor was there (did he or anyone besides Trip even care?). The other thing was the captain's ironic berating of Trip, and the fact that it seemed to me that the only reason why he was so willing to look the other way was because of their technology. Now, what does that say about our dear captain? Not much at all. The hypocrisy.