I agree with Goober's reasoning regarding the Terrans still possessing some Avenger prototypes, allowing the Plato and its original mission to be retained.
I suggest that you have the player as part of the Taurus' escort, just play with the timing a bit. Have your group arrive just as the first wave of Vasudan ships are attacking the Plato. When they are all shot down, your wing is ordered to make for the Plato to first shoot down the escort, before bombers will move in for the kill. As you reach the half-way point between the two ships, the Shivan wings attack the Taurus and the player's wing is ordered to abort the attack and defend the Taurus. The player gets back about 30 seconds before the Shivans destroy the Taurus. The player will have an opportunity to destroy a Shivan craft (fighter or bomber) for the bonus objective. Once the Taurus is destroyed, the Shivans jump out (as they do in the original). Vasudan command is still a bit shocked, and is considering recalling your wing (given ship-guardian-threshold to ensure that enough ships survive to provide dialogue sources), but a wingman points out that they still have a job to do... destroy the Plato. As you head off to engage the Terrans, the Shivans attack the Plato and its escort. The engagement there gives the player additional opportunities to get the bonus objective for the Shivan kill. A final bonus objective is to destroy both of the Plato's escape pods.
On another note, we never actually learned what the circumstances behind the original theft of the Avenger prototypes was. It might be interesting to create an additional mission (perhaps an alternate to the FS1 asteroid mission) covering these events. Maybe they were piloting captured Terran craft, operating on intel they received from McCarthy.
Just a thought, but if this project is getting enough backing from the Port team, perhaps it deserves its own sub-forum just like ST:R. That way, each mission's discussion can remain in separate threads to avoid confusion.
Later!