What was with the harsh Reconstruction?

Alright, I understand how the southern states needed to be disciplined due to their actions in the Civil War, but I wonder what was going through Congress' collective heads as they passed a Military Government Bill. The President vetoed it on the grounds of unconstitutionality, but Congress was able to overrule his decision. I don't quite understand why. And where exactly was the Supreme Court to put an end to that madness before the ball got rolling? People say our Congress today is corrupt, but the events of the late 1860's were insane.