Reference letter request for options the letter writer is unsupportive of
I think this dilemma can be approached from first principles: a letter of recommendation is an explicit choice to support a person on the path that they have chosen.

In most cases, the main question is not the path but whether this particular person is a good match for that path.  If one didn't like the path, however, I think it would be vital to come back to the question of how much you support the person.

Sometimes, we support somebody enough to want to help them even when they are on a course that we have grave doubts about: many a parent has faced such dilemmas, and a teacher's role can sometimes be quite similar.
Other times, we might find the path itself so problematic that we refuse to support, even if it means doing damage to a person's hopes and dreams.

In short: I don't think there's a cut and dried answer, but that one must judge the individual situation with the question: "Can I, in good faith, support this person's decision to take this path?"