Typically, being the main villain would mean that Negan is destined to die. He's the one heading up the other side of this conflict, so if Rick is to win, surely he has to take Negan out, right?
There's sound logic to that, but Negan is a huge part of The Walking Dead's world. While the on-screen results have been mixed - Jeffrey Dean Morgan is a good actor, but the character has been too one-note thus far - he can continue to influence things beyond this year.
That cell has been built for a reason, and Morgan's death should be the catalyst that sees Rick refuse to kill Negan, and imprison him instead.
Looking at the other option, there's potential for a big surprise there. Negan was built up for so long that people might expect him to live beyond this year, and killing him off could be a subversion of that (and certainly of comic fans' notions). There's also the fact that it's harder to keep a character sitting in a cell on a TV show than it is a comic, and JDL is a well-regarded actor who'd have no shortage of other work, which could force their hand.
Ultimately, though, I think they'll have big plans for using Negan in the future, even once the war has been won.