I do not think, that this will affect Freespace anyway. It is the same after THQ bought Volition back then... you never heard from Summoner 3, Descent 4 or FreeSpace 3 again.
And i have to say, i do not want a FreeSpace 3... a few years ago one from HLP interviewed one of the
guys and we know, they never thought about how to solute this shivan problem created in FreeSpace 2 with a fleet of juggernaughts that can blow up stars or what happened to Aken Bosch.
We have many theories we can play in fan-made campaigns and we can choose which continuiation we like the most. An official sequel could destroy it, i think, because we would know "No, it is a complete different story". And because
do not have a master plan when they created the story of FreeSpace 2, they would think about a story for FS3 only today, where their thoughs can be already influenced by Blue Planet, Inferno or other "Sequel-Total Conversions" they heard of... i do not think, that this is worth it, at all.
I think the best official sequel is, if there are no official sequel... :-)