Was playing around in the mission "In light and Darkness from the mission pack and though I'd let you know a few things worth noting.
First, like a few others have mentioned, you can tell ships in this mission that are friendly now and be hostile later to jump out (including the space station in this one too, was cool to watch)
Second, I found this out from playing around. Because I told the ships to jump out, I couldn't finish the mission so for no reason I decided to disable my friendly ships. after getting bored with it and finding it amazing the ship had enough power left to jump out, i jumpout to end the mission and get the you're a traitor screen, blah blah. Now this is the important part. The text is from the normal FS2 you're a traitor thing. Didn't know if this was supposed to be different or not yet, but thought you'd like to know that at least for the "In light and Darkness" single player mission, it still tells me both terrans and vasudans want me jail/killed/whatever. Like I said, just a small concern, nothing too important for people not trying to friendly fire their own AI but something to look into to finish up converting the program into the B5 universe.