Voyager and Enterprise both did this on a number of occasions, though the TOS/TNG/DS9 crews weren't completely free of it either. They set up an EXCELLENT moral dilemma but the way they resolve it makes the main characters either look like first class jerks, just plain stupid, or some combination thereof.
These are usually the episodes that are still stirring up debates years later. Sure the heroes aren't always going to be perfect, but there's a huge difference between making a morally questionable choice because you have to and regretting it and just not giving a damn or reveling in them.
In the case of this episode, I get the fact that it's not Archer's call to make. He's establishing first contact here. But literally condoning the exploitation of a significant number of people in another species? At the very least he should have told Trip it's not their place personally to make a call there, but he's going to recommend Earth put diplomatic pressure on them because slavers are not the kind of people they want to be associating with. The way Archer did it, he probably would've been alright if he made contact with Nazi Germany who was in the process of gassing all their Jews.
All I can tell you S/U Fan is look out... some Archer's biggest bad calls are still yet to come.