I, for myself, use one of the biggest flaws of the game to counter auto-repair - Focused fire.
You can't avoid getting your units to concentrate fire on a target that doesn't quite *need* so much firepower. Killed units don't repair themselves, therefore using a combination of moderate ROF weapons, such as HPV, with high ROF weapons like assault gun (twin assault gun whenever you can get it), using a commander, you can focus fire on specific enemies, they'll get killed, the cannon's splash damage already drained a bit of the life of the units around, and you are ready to designate a new target.
The weak point of relying on auto-repair is that you must have a break: the enemy must stop sending whatever units he is for you to repair yourself. If the units move or start firing, they already stop auto-repairing for a while, and since it's concentrated fire, probably all of the units on the repairing group will stop auto-repairing to fire the attacking unit.
Having that in mind and focusing your attacks on particular units so that they die and doesn't get the chance to auto-repair, should avoid too much stress about it.
About the concept of auto-repair, then the mobile repairing units would also be illogical, because IRL nothing can be repaired up to 100% of its original form.
Perhaps you should add a "Time to Die mod" (

) where there are no repair features? xD
I think that would be interesting, but I wouldn't like a mod that only removed auto-repair.