About Darkseid's Omega Sanction:
Batman was nailed by Darkseid’s Omega Sanction, rays of energy that transport the target into a series of successively worsening alternate lives (as shown by Morrison in the Seven Soldiers: Mr. Miracle miniseries in 2005-2006, and stated plainly by Darkseid in Final Crisis #6). Of course, taking a closer look, which is always a good idea with Morrison’s work, you see that the beams nail Batman in the head and the heart which probably has some meaning.
Over the course of Final Crisis, Morrison has proven himself to be a major Jack Kirby (Darkseid creator) scholar, and as such, has adopted the Omega Sanction from Kirby's original use of it back in Forever People #6 ("The Omega Effect!"). In that story, Darkseid hit every member (save one, Serifan) to various points in time, where they’re all later rescued as shown in Forever People #7. Morrison himself even plays with the fact in Final Crisis #6 when Sonny Sumo discusses coming from a “Lateral Universe” with Mr. Miracle, Shilo Norman. Sonny was sent back to Feudal Japan by Darkseid’s Omega Beams, where, as Kirby showed, he lived a happy, full life - the "Omega Sanction" was apparently later refined to be a bit more sadistic. Sonny’s back in his original state, he explains, due to falling through a hole in his life into that Sonny Sumo’s life (no – there is no pronoun trouble in that sentence, Elmer Fudd).
Long explanation short – there’s a wide open backdoor to Bruce Wayne’s “death” that Morrison is even hinting isn't final in the same issue where Batman “dies.”