Smoking isn't even bad for you. It's just inhaling smoke, which isn't "dangerous" od "unhealthy". It's all a conspiracy to shame the superior race of smokers.
It fades after a few episodes. I haven't watched it since aired, so not sure about what point, but I do think it's been mostly fazed out within the first 5 or 6 episodes. There's an actual character purpose for the quirk either way.
Oh shit, the movie came way before the spin-off. I don't know why I thought the spin-off was first.
I'd at least argue the movie fundamentally revolved around Haruhi even if she was absent for a large chunk of it.