Is this a 4v4 specific problem? I can't help but think it is.
I figured the natural penalty for having to repair vehicles is tying up the vehicle AND the repair squads who can't cap/fight/mine while doing it. It's a time penalty, which is also a resource.
In 4v4 it's often to see 2-3 heavy vehicles which kill everytinh on their path, make enemy bleed, and when hp bar is lower than 50% they just reverse to point where 3-4 engi squads are reparing those heavies. It's really frustrating. Getting vet, killing enemies, no bleed, no penalty for bringing KT to 10% hp.