In my geeky-ass, personal Trek universe, Tom DID get the promotion, but then was busted down to regular Lt. after the events of "the Pegasus" were brought to light.
He didn't come forward like Will did, but never got the same chance Will was given to make amends.
The JAG justice's head nearly exploded contemplating the philosophical ramifications so just gave him a slap on the wrist and bumped him down a notch.
