I like the setup you provide, Keith. It would be pretty easy to have the player get a set of "last known" coordinates, and let the player look around for a while. What I picture is this:
"The ship was last reported near quadrant C2"
Then the player takes his ship there, and there is nothing around. Once the player arrives, a timer starts, say perhaps 60 seconds. After the timer expires, SCI gets a reading of some space debris near a nebula in quadrant C3, so the player moves there. (For the sake of gameplay, we could use the model of the anomaly for the debris) SCI reports that there isn't enough debris there to be the ship, but it could be the result of a battle.
COMMS now intercepts a transmission from a Torgoth cruiser. The message is incomplete, but the idea is that they are pursuing something into the nebula. The player moves in, but once inside the nebula, warp doesn't work, and perhaps even torpedoes go out. The player is now forced to watch helplessly as the ship they were trying to save is set upon and destroyed by Torgoth cruisers, just our of range of the players ability to get there in time under impulse only.
As the enemies warp out, (Which we could simulate by giving them a "direct" command and incresaing their top speed) COMMS reports that they received one last message from the ship.
Pretty much a re-telling of what you said, with a few more specifics, but that's all I could think of. (I have to go fix my stupid car again...) But it shouldn't be too hard to script.