Battlefield 1942 may be the most modded game in history. It's not open source, but like someone asked for, it has tons of good modelling tools. The game engine would be well-suited for FS style conflict (open warfare as opposed to tournament matches or covert ops). Creating a FS mod in BF1942 would be as simple as coming up with a few new models for Vasudans, Shivans and Hallfight-looking Terrans. Plus a few new levels, if you aren't happy with a simple desert or city landscape.
I really fail to see, however, what would be so original or great about an FreeSpace FPS. Probably the only cool thing would be seeing Vasudan and Shivan melee skills (although that would be very awesome in itself). There are plenty of other sci-fi shooters out there.