No way Warner Brothers, who want to make as much money as possible on their high-profile Superman cinematic revival, would risk not adding the extra pay bump to see Henry Cavill throw a super-swing or Michael Shannon's Frankenstein exterior (Great actor and I'm sure a great guy but come on, he looks creepy!) in three dimensions.
Yep, The Man of Steel will be in 3D reports the official IMAX site.
The studio already has their justification. The jaw-dropping receipts of The Avengers and the good-but-not-great grosses of The Amazing Spider-Man this past week. Zack Snyder might hate 3D (God love em), but this wasn't his call to make.