On the other hand, if they are out of the fleet, their options for sabotage are a lot more limited than on board of the military ships and stations. Allthough one could argue that the GTVA might rather have them, where they can keep an eye on them.
Split them apart into small groups, spread around the fleet under discreet surveillance, rather than allowing them to go to ground and form large resistance cells, hidden well in their own hometerretory.
A delicate balancing act without an obvious right or wrong way awaits the GTVA one way or the other, if they manage to take controll of Sol.
... I just had a rather outlandish though. Very unlikely but mabe worth a discussion.
What about letting the Vasudans police the Sol system after the war, to avoid anti GTA activism? You know... keeping the factions that killed each other seperated for the time being and letting the neutral faction act as a buffer.