I really would have liked this story to end with the creation of a Mary universe. Or that the twist would have been that Mary and Jerry were so close together they expanded into a single brane and made a Mary-and-Jerry universe. Either of those would have ended the story on a somewhat more ambiguous note - there could be a hope of redemption for Tom, as Mary or M&J could recreate the universe without making his mistakes - but it would by no means be certain. As it is, the story ended up simply being "Tom's desire for revenge backfired and destroyed all he attempted to preserve" which is perhaps more classically tragic but also less interesting to my modern sensibilities than a more open ending.
Also, for all his computer power, he really wasn't that smart, right? I mean, he killed his alternate *while* Mary was cheating on him. Even if he managed to save her, she would have been wracked with far greater guilt than she would have otherwise. The promise of happiness for both of them was obviously gone with him dead, but he would have made a serious dent in her prospects for happiness at all. Or pushed her to be be with Jerry. Did that never occur to him in the millions of years since his change of heart? Couldn't he have tried to deflect both meteors, aiming the first one at the tachyon machine instead of his head, or something?
That said, reservations about the ending and plot nitpicking aside, I did think this was a good, clever story, that kept me interested throughout even as I got progressively more annoyed at Tom and his stupidity.