Sadly that is something I (and others) have suggested several times.
For some reason the F/A switch for the SRV can be set to either state as "default" in the options, but ship's assists are always default On, which is more than a little frustrating when you are an F/A off pilot.
But it's better than it used to be, previously the F/A turned back on every time you dropped from SC. Now THAT was annoying. At least now the game remembers my setting for the duration of the gaming session.
Small victories, I guess.