Answer #1: I think he'd be an easy target for a mob uprising. As soon as the first wave of famine, disease, etc. struck, it would be very ease to blame Baltar and tar-and-feather (or worse) the guy.
Answer #2: How will Osama Bin Laden be rememered 100-200 years from now? As a terrorist or as a hero who restored Islam to its glory? Probably depends on who gets to write the history books or where in the world you are reading them. Same with Baltar. Cylon dominated settlements might rememeber him as a hero. Human dominated settlements might remember him as a terrorist.
Answer #3: fast forward 150,000 years in the future, and nobody remembers him at all.