Oh, definitely.
Batman isn't the "bad guy" at all. He's a hero. Just for this movie, he may be a somewhat misguided hero. He's still doing what he believes is right.
Yeah, if we're right, then I'd expect Batman and Lex to begin the movie in an alliance. Lex manipulates Bats until The World's Greatest Detective does what he does best, and figures out who the real villain is.
Frankly, I think that'll make for an epic story.