The Gordon/Batman dynamic has been done so many times at this point, we wouldn’t be surprised if Warner Bros. opted to bring in someone new like Ellen Yindel from The Dark Knight Returns, or even an older Barbara Gordon, much in the same way that Batman Beyond used her.
Killing Commissioner Gordon at some point in the future is also feasible simply due to the fact that there’s precedent for replacing him — particularly when there’s an older Batman involved.
However, beyond that, he becomes one of the more expendable members of The Bat Family.
We already know that J.K. Simmons will premiere in next year’s Justice League, and it seems fairly likely that he will at least continue on to work with The Dark Knight in the first solo Batman movie.