Hi Exel!
This point pops up every now and then, and there are aready some easy answers:
First, you can deactivate individual weapons on individual units, so if you want a tank not to fire its cmg, turn it off and it won't. A pain to do this on a large scale, but well...
Secondly, there IS an advantage in firing small arms at 50in.-steel tanks. Even when unhurt, the crews gain suppression every time their AFV gets hit. So even if you have no AT weapons, you can pebble a tank senselessly until it takes fright and runs away! You can even expect a track hit and immobilisation.
This being why infantry squads also fire their rifles at tanks.
So shooting at over-armored units can prove useful indeed.
Anyway, I don't think you should expect any big code overhaul over this very point. I'll let the designers talk about this,so you'll see by yourself.
Mmh, talking about this, maybe twiddling in some switchable and parameterized 'no-effect' limit under which units won't fire since they don't have a chance (with input like speed, stabilizer, armor, hit prob., etc.)...