Once Batman and Superman set aside their differences, and they hopefully will, it should be to stop a greater common enemy. Batman's beef with Superman might fade once, and if, he learns that the destruction in Metropolis was not entirely his fault. If Snyder follows Miller's Dark Knight Returns format, and Batman does in fact beat Superman in combat, it may make Batman rethink his idea of wrong and right and why the two are fighting in the first place. If he's able to bring a super powered alien to his knees perhaps only then will Batman understand Superman isn't guilty for the destruction he caused. If Superman has Batman's sympathy, and Batman has done the proper detective work, it'll be clear the enemy is neither one of them. And if Lex and Bruce are working with a shaky alliance in the hopes of rebuilding Metropolis, we might see Lex's exterior crack and his true motives revealed.