Ive been thinking that we don't know for sure that it was the Galactic Authority that captured them as the goons in black don't exactly look like official police types even if they are some kind of special tac unit, also as was mentioned in six's flashback the terrorist group managed to steal a GA cruiser. This could well be part of Six trying to buy his way back into the terrorists good books as part of a bigger plan.
I never even considered that. It could be the terrorists and it's possible Six will free his friends pretty soon in the second season premiere. I'd buy that more than him just handing them over to the GA. Then again, he did seem pretty upset over the planet getting destroyed. Also, welcome to the board.