[Klemm]

There is an option called "Autopilot automation" or so in the controls menu, which must be assigned to a key. When pressed, it does just this, it turns the automated autopilot off or on. So when switching to another position the autopilot DOESNT take over. This was always in the game.
So NO need for a mod. Just a bit of looking through the controls menu.

And the solution to the autopilot dropping your bombs when you plane is hit is to never engage it in the mission. I agree, thats annoying, but there is no other solution. The autopilot still seems to have some control over the plane when it was turned on and then off again.