I think there is merit to a prequel game, but the mistake would be assuming the formula that works in Freespace will work there. Most settings can work, if you play to its strengths, but that means having the freedom to build mechanics and ideas from the ground up.
Just off the top of my head, a space RTS / grand strategy type game could probably work pretty well with the Terran-Vasudan setting. Instead of controlling a single fighter, you'd control entire fleets, sending out strikecraft wings to various missions or picking what kind of technology to research. Perhaps some personel management could also be implemented. There's plenty of behind the scene damage control action happening all the time in Freespace that we never get to see.