The problem I have with fixing the damage in the pits is the very minor stuff. You get tapped in the rear in T1, small damage to the back. No big deal, not you're fault either. Later you clip a tire at the apex, again small damage to the front this time. Again, no big deal. You didn't crash and shouldn't recieve any penalty for it. Now you're coming to the last lap in 1st place. 2nd is a good bit behind. You realize you have 2.0% fuel left and running 3.5% per lap. Hit F12, setup for a 5% refuel and jump over into the pits for a splash. WTF!!! It's fixing damage!!! 5 seconds on the front, then 5 seconds on the back and there goes 2nd and 3rd place cars on by!!!
I can see using the "fixing damage" in the pits as a penalty when you crash. But even if you have minor damage not from crashing, but from close racing, getting tapped by someone else, or just clipping a tire barrier somewhere, it shouldn't ruin your finish because of the "penalty".