I think the character decisions were motivated, intentionally difficult to wrestle with and especially relevant for the time it was made. I think what makes the show unforgivable for it however, is the complete lack of consequences for those transgressions.
And before someone brings up DS9 and In the Pale Moonlight, I would point out that that entire episode was doing the work of questioning and condemning decisions just like this. It's what ENT was missing.