But there's a difference between a story where you disagree with the characters' choices and a bad story. If anything, many of the best stories are the ones that challenge our morals, that face us with characters making choices that we feel are wrong or that make us uncomfortable. As I've said, I'm not crazy about the decision the characters make in "Dear Doctor," but I still think it's a good episode, partly because it dares to be challenging and take us out of our comfort zone.
I personally think the way their decision is presented in the episode does
make it a bad episode because it seems to be portrayed as absolutely right with no ambiguity whatsoever.
yep. Considering the end decision, nothing was going to salvage the episode, but if they'd actually portrayed it with ambiguity, like maybe we're supposed to think Archer made the wrong call, that would have been interesting. Actually, the original ending would have been more interesting and much better in the sense it would have at least let Archer off the hook.
Instead, as you write, there's no ambiguity. We're clearly meant to think that the right decision was made, and Archer is well on the way to realizing the wisdom of a future PD. It's absolutely terrible instead of just mostly terrible.