Install a small (.1) active scanner on your AMM. If their target pops, they will seek out a new one.
I had that. They didn't acquire.
Edit:
While thinking, I've had a few more ideas for things I'd like to see. These are pretty much all things that used to be in aurora, but aren't any more.
1. Missile control. I'm not sure why this was removed (balance or code). If it was for balance, I have a suggestion. Instead of allowing all missiles to be retargeted for free, I would make multiple levels. The most basic is a simple destruct switch, either automatic, or very cheap and no mass. Above that, you might be able to do retargeting to targets detected by onboard sensors, and finally is full control with maybe .4 MSP and a decent cost.
2. Mothballs. I ran across a mention of it, but discovered this had been removed. It seems like it might be useful for older ships, particularly ones it's not economical to refit (engines, etc)
3. Exclusion zones. I read about them in the diplomatic rules, but I believe they can't be done anymore. This is something that seems realistic, though, and might prove useful.
4. Clean warheads. This is new, but it would work sort of like the opposite of enhanced radiation warheads. You sacrifice hitting power on the target for reduced radiation and colateral damage during planetary bombardment.
Edit 2:
Orbital Weapons platforms, like PDCs but in orbit, would be nice. I know you can do them now, but it takes shipyard space, maintainence at the destination, and you have to move them. This way you could do things like lasers for fixed defenses.