Actually, the NTF are in a damned good position at the beginning of FS2, their forces control multiple systems, and they've managed to swell their ranks with ships from over 4 different Terran Fleets, and let's not forget Petrarch's little "we are looking at a decisive victory by the NTF if nothing can be done" after Rear Admiral Koth launches an attack on Epsilon Pegasi. Had it not been for the Colossus, the GTVA would've been in SERIOUS trouble (i'd have given it two more months of Civil War before the strain of the Shivans and the NTF caused a catastrophic split between inside the GTVA, possibly sparking a second T-V War).
So, since the NTF wouldn't have known that the Colossus would annihilate them after a few months when the rebellion began, i would have definitely defected, no questions asked...
...lest those darn Vasudans nick my Head...