Killing Batman isn't such a bad idea. It's an obvious idea, perhaps, but it's not without its merits. A much more radical idea would be Bruce Wayne abandoning the Batman moniker (his work is done, or rather can no longer be done), and that could be less satisfying.
The third alternative is an ending that is not an ending; that is, Batman is still out there, but the third film wraps things up thematically somehow. That does leave more wiggle room for a non-Nolan fourth picture to suggest it's a semi-sequel, though.