I think the problem in "Surrender, Belisarius" was that the transports needed to flee the planet, but were incapable of jumping themselves, and no recovery vessels were available at the time the mission started. If the Psamtik had larger problems to be concerned with, of course it wasn't just going to immediately jump to the transports' position. By the time it was available for the recovery operation, the transports had already put a fair bit of distance between themselves and the planet.
If you want to bring up technical details again, it's worthy to note that it's very difficult to make a mission occur near a planet in retail FS2, given that you can only stretch the planetary background images so much before they start to look downright ugly, and you have to do a lot of scripting to even begin to simulate things like re-entry dangers and ships hiding behind the planet/moons. Heck, you really couldn't even simulate significant amounts of movement relative to the planet, since you couldn't/can't adjust the background on the fly.
While it's nice to have a description of how subspace drives work, and I've given myself a rough outline to use in missions, the fact of the matter is, it's fictional technology that's used as a plot device. Volition wasn't always consistant in how they used it, because the plot demanded it be used in different ways. For example, despite decades of advances in subspace and navigational technology, the Psamtik still managed to miss its mark by 9000 meters in the nebula, so that they'd be in perfect position to be annihilated by Sathanas number two, and it's never clear when fighters can make intersystem subspace jumps versus when they have to make intrasystem subspace jumps.
Volition FRED'er: "Yo! You said the Psamtik should get shot down by the second Sathanas here, but when that Sathanas jumps in, it needs several thousand meters of glide-distance from the second Knossos."
FS2 Storyline Director: "The....ummm....subspace disturbance of the portal.....errr.....disrupts the Psamtik, so they're 9000 meters off the mark."
Volition FRED'er: "That's weak and contrived, and you should be shot where you stand."
FS2 Storyline Director: "You're weak and contrived, and I can fire you where you stand. Suspend their disbelief, or perish!"
Volition FRED'er: "*Sigh* Nine-thousand meters it is...."
While there may be less hate and malice in the real version, I've no doubt that that kind of scene played out a number of times, with the topic of subspace at its core. I'm sure many user-made campaigns have had such discussions between team members, or between the lone author's inner FRED'er and story writer.
BlueFlames' Split Personality #1: "Yo! It's going to take for-freaking-ever for this convoy to cover the thirty kilometers back to the node they entered the area through!"
BlueFlames' Split Personality #2: "The crews can.....ummm.....apply more power to his subspace drive to.....errr.....jump out far from the node."
BlueFlames' Split Personality #1: "That's weak and contrived, and you should be shot where you stand."
BlueFlames' Split Personality #2: "You're weak and contrived, and I don't think you fully comprehend the implications of your proposed course of action. Suspend their disbelief, or perish!"
BlueFlames' Split Personality #1: "*Sigh* 'We need more power, Scotty,' it is...."
Actually, if the Volition version played out anywhere near like my version, there was more hate and malice involved, but that's neither here nor there.
The point is, sometimes you can come up with a nice, cushy, consistant explanation for why something is the way it is. Other times you just need to accept the plot device for what it is, so that you can move on.