How about switching "Doc" from "Love Boat" with McCoy? Or switching McHale's second-in-command Chuck Parker with Riker?
This is a fun idea for a bit of humorous discussion, but I don't think the concept could work on screen, as the Trek Universe reality would not allow someone like Smith (as portrayed in all but the first few episodes) to ever end up in most any sort of position in Starfleet, not to mention rising to chief medical officer. Reg Barclay is about as close (I think) as we could come to seeing a Smith-like character in Starfleet, but Reg can only exist there because of his mind & technical abilities. Smith was portrayed by having no such redeeming gifts.
Smith's original nasty, treacherous saboteur persona wouldn't have fit in, either, in my opinion.
... But the "lovable"(?) annoying characters like Lwaxana Troi, Q, and even Neelix were never my favorites on Trek.... and since Dr. Smith is the King of Irwin Allen's annoying characters, maybe that is why I am not seeing this match-up as working very well!