Well in the end there are several branching campaigns for Freespace.
In Pandora's Box there were three mission trees that were reachable by an SOC choice during the campaign.
The never finished Unholy Alliance had a very complex mission tree that was only reachable through mission objectives. AFAIK it is the longest campaign in Freespace with a mission tree as it has already 40+ missions in its unfinished state.
Campaigns like Crucible were also a branching ones, but only used a sequential campaign for that. It did not have a mission tree, but used countless of events that refers to events in the previous missions which actually change the whole story and missions in the later campaign.
Actually i think that this kind of branching is much better instead to create a ton of unique missions most of the players will never play.
FreeSpace: The Great War was also a branching campaign in the same way, because events in one mission had sometimes it's effect in the next mission. If the Mecross goes down in Exodus, it can not help you at the defense of the Hope... and if you lose the Hope the Pinnacle will be present in the next mission. Actually i am curious about how many players have continued the campaign after the Hope was destroyed in "Last Hope".
Actually i am not sure if FreeSpace 2 have any other branching events except "How many beams have the Sathanas in 'High Noon'?"