If you can get all the financial, trademark, and legal hassle out of the way i'm sure all the modding community which is still as strong as ever will be glad to help, take disco itself as an example. you would be surprised just how many space games whether they be RTS, Simulation or whatever have active mods still being worked on and are being loved. biggest problem is with the vanilla FL storyline it rapped allot of things up in the end, left very little to go on with.
Forget about getting the sources. It is still being sold online and that means there are contracts, most likely longterm, that bind the holder of FL digital property. So they cant, even if they want to.
If you care so much, collect some money and/or motivate some professional assembler magicians to fix bugs and extend Freelancer. To them the available exe is as good as "the sources" to a common #c programmer.
Any new information relevant to this issue would be very helpful. If someone could contact the relevant department at Microsoft by phone or email, that would be great. I do not have time at the moment.