Given that the game is about 10 years older than Freelancer, and that the original developer has since disbanded and the publisher is not Microsoft; either it passed under the corporate radar, they have permission, or nobody cares anyway.
I don't think carrying over freelancer to SC will help Disco, it may be better to start fresh with the new material and create something different with it.
Well why didn't I see this thread before? Well anyway, as I mentioned it somewhere before.
There could be a total "filtering" of the story, as in. Nomads fully take over Sirius, finaly at once. The Humans are forced to escape, it could be again sleeper ships, thus they make a last hope into surviving. But strange thing happens that their jump calculations experience an error and it sets coordinates to Sol. They jump into the direction of Sol, however a disturbance occurs while jumping, they reality shift/swift whatever (could be even a timeshift) into the Universe where Sol didn't got destroyed, but odly, it's dead. No life signs at all. It even could be that Humanity got wiped out in that reality by Aliens (Vanduuls and all those present in Star Citizen) and the Humans from Disco universe would repopulate Sol, slowly advancing (the Star Citizen Ships as you see would be new ship types), while small parts of old Ships from Freelancer would be kept, Discovery could continue on that point from Star Citizen Universe.
The Official Factions could be implemented and a weird Campaign could start from that point. This way, we wont have to completely redesign Sirius or the Bases and all which would probably take ALOT of time and Effort (unless we can find more Devs that are willing to work together on this).
So the new Discovery mod would start from the point on where Star Citizen started in Sol, kinda like you guys said an alternate reality. Of course, the RP could be done that some Wilde boarded the Sleeper Ships and would soon depart building their own force awaiting the day of the Nomads return. Maybe even Nomad/Human hybrid ships, at least this way Nomads still could exist in the game as playable characters, only difference is, you gonna be a Wilde, not a K'Hara.
2nd Option:
Again Nomads take over Sirius, Humanity's last hope, their Origin, Earth. Prepare Sleeper ships launch into Sol. I think we could either remove all planets until Pluto, that should be possible and Sol could be repopulated by all the debries and Stations could be build to sustain Life (Zoners were always good in this, living in Stations and all, so they know what to do.) This way, the story could start from there on with Star Citizen ships how humanity meets different alien races suddenly which previously fought the Daam K'vosh? Vanduul and all, could be implemented that they were one of those Alien Empires that battled Daam K'vosh.
Thread locked for gravedigging. Go find one of the two newer Star Citizen threads.
(Also, if there's ever going to be a Discovery Star Citizen mod (still pretty unlikely), we're probably not going to bother doing something ridiculous like porting Freelancer's story into the SC engine.)