I was watching some of the clips online and it seems that Tommy is not a bad guy in this one... If you look at the character clips (Flint's) you will see Tommy in the corner of the screen (it is at Joe Colton's place when they are planning).

I'm betting he makes the allegiance switch in this movie. He's definitely Cobra for some of it.

Agreed. I am betting after initial prison break for CC he finds out about his betrayal and that is why SnakeEyes 'rescues' him from Red Ninja.