Nothing you can do about modifying follow orders, or weapons orders for ships. there is an autofire option, but it is more for the ai. Fighters should rearm and refuel automatically upon landing on their carrier craft though, that shouldn't be an issue. The subspace bubble option(on the contacts tab) is probably the most helpful thing you can do. It will turn off the rest of the galaxy and let you focus on just the fight, which speeds up turn processing. Subspace bubble requires SM mode to be on, so turn that on, close the system map if it is open, and re open it, and the option should appear.
If you feel that you're totally outmatched and don't want to wait for all of your ships to die you can abandon those via the f6 menu.