The way I read Franklin's quote is that if someone says "well, (factual statement X) is true, and from it I draw (unwarranted conclusion Y)", we should claim to agree with him (because we agree with X) and act as though drawing conclusion Y is a minor flaw in his theory that doesn't negate the fact that he's basically correct.

But he's not basically correct. He did invoke X, and X is true, but to say that he's right, or even partially right, means he's right about a substantial part of his argument, not that he's based it on at least one statement that is true. A homeopath doesn't become partly right just because he says "well, vaccines work by using a tiny amount of something to protect against it, so perhaps homeopathy can also use a tiny amount of a substance to protect against it", even if the statement about vaccines is literally correct.