If he's assasinated at any point I imagine he'd be considered great by virtue of his martyrdom. Maybe a sort of 19th century JFK?
I don't think martyrdom alone grants greatness; look at how Garfield is perceived, as an example: mourned greatly in his day as a martyred president, but almost a footnote in history today.
IMHO, if Lincoln managed to somehow lessen the horrors of the "War Between the States", or to manage to diplomatically persuade the C.S.A. to come back into the fold, he would be remembered as a greater figure than we think of him today.
He might achieve the former by controlling some of the more hawkish military leaders of the day, instead of allowing them as much free reign, perhaps? Thus, leading to less resentment in the South.
A victorious Confederacy might not be as difficult to persuade to rejoin the Union as you might think, although it is most probable that a core confederacy would remain outside of the Union, with border states trying to figure which side their toast would be better buttered by.
Just remember, a Confederate victory does
not necessarily entail the success of the C.S.A. as a nation. The earlier you have a Confederate victory, the less likely it is that the several states will feel united in their efforts to survive against the Union.