The GTVA wants integration (and the destruction of Ubuntu, as much as can be completed) not outright occupation. I highly doubt they would disbar all active or reserve military personnel from serving, and doubt even more that the subject population is even large enough to be a blip. If we go with a ballpark five thousand figure for crewman per frigate, double it for destroyers, and half it for cruisers, That'd be approximately 400,000 crewmen. In the Sol system of the late 2300s, that's more than likely a fraction of a fraction of a percent of the system-wide population. Hell, that's a fraction of a percent of just the Earth now. I have a hard time believing that the active shipboard personnel of the UEF is much over one million at the largest, and that's even pushing it (merchant marine excluded). If every single one of those crewman were barred from further service, and assuming a workforce of approximately half the population (for today, which is also probably low), the increase in global unemployment would be somewhere in the neighborhood of 0.02%. In Sol of the future, it would be even less than that.
This all assumes that the GTVA wouldn't lay off shipyard workers, installation workers, and the like, because I have a hard time imagining a more stupid thing for them to do.