I would be fine with a fully functioning AFMU so long as it doesn't work in combat. I voted yes it would be too powerful in the poll because repairs during combat would be over-powered, but allowing the victor of an engagement to right his his/her ship once the fight is over would be great to ward off the "hurry back to get revenge" issues that can happen right now.
The general consensus seems to be that it would make for a valuable, non-overpowered exploration tool as long as it takes a while to repair damage. A solution could be that hardpoints must be retracted in order to use the AFMU and that critical modules such as thrusters take an extended amount of time to repair (eg. 10 seconds per damage percentage) to avoid it from being useful in combat.