I dunno about the "Jon Snow is probably not Ned's kid" being all that obvious for a good portion of the books; I think it's mostly just accepted by the fandom that that is the case. There is some decent evidence that he is, even though I don't personally believe he is. But I get what you mean.

I don't know how I'm going to feel about the rest of the show. I guess it depends on what else they change that they didn't need to change. But I would be seriously, seriously surprised if they addressed it, considering they don't feel like they did anything wrong.