Well, it looks like my feasibility tests for "flying the carried fighter" were incomplete.
Right now, it works, but there an issue when your fighter dies, and you are ejected.
See, your carrier does indeed go rogue - that's not the problem. The problem is that he stays in the system and won't warp out.
You have a mission that you abort to call for the carrier to warp in. (It's disabled, and you dock with it, and this will reset you to be able to hop into a new fighter) But things look real odd when neutral carriers start to populate the system.
They don't warp out presumably because they have 0 speed and 0 accell. And I can't give them any positive number or they will follow you at your full speed when they are launched. (looks like you launching out of it) With 0s, they stay put, and you can fly back to them to dock and re-arm, change fighters, etc.
Now I might be able to pull some trickery with your fighter self-destructing on launch, and you "escaping" into the fighter you've chosen to fly. In this case I can give the carrier normal speed and accell, and he'll warp out eventually, if I can make sure he doesn't try to visit any stellars first. (Tips, here?)
But launching out of an "escape ship" seems to give you a random drain on your shields and armor, and I'm not sure how I'm going time the replenishing of these.
Then you always interface with a disabled carrier if you want to re-arm, change fighters, etc.
This leads to my second problem, which has a couple of different angles to it.
Re-arming at the carrier.
If I make the carrier weak, there are going to be some shield/armor issues when you dock with it when you're near death. Any shield or armor mods attached to the carrier outfit are going to take a moment to kick in - and I'm not sure they are working properly. This can cause some unrealistic deaths.
If I make the carrier strong, then the player can just sit in it, and let it's defenses take out the enemy.
Neither of these situations is very good, and I'm not sure of the best compromises to pull this off.
At any rate, if a good solution isn't found, the "fly the fighter" idea may be scrapped.