I don't remember how long crater's remain visible, but it's not particularly long...no longer than the hangers remain down, which is 15 minutes. As all bombing will be less accurate, including JABO'ing, it seems reasonable to bring back damage from hitting craters. It will be harder to put a bomb crater write on time of a spawn point to prevent launching, and you've always got the option of launching from a different spawnpoint or from the hanger. Yes, the auto-take-off folks will suffer, but they're at a disadvantage anyway. They are easy meat for vulchers as it is. Hitting the edge of a crater without actually entering it's interior should cause landing gear damage above certain speeds. Entering the interior of the crater should cause a crash; again, the speed at time of crash should determine if you die in the crash.
This is IMO much better than the idea of "destroying" the runway. I'd also make the ability to take off from "off-runway" dependent on the weight and power of the aircraft, as well as a function of the terrain "friction" or roughness. A clean fighter with less than full tanks should have no problem, but a bombed-up heavy fighter with full tanks should be unable to gain flying speed "in the rough." Also, there is always the taxi-ways that can be used as auxiliary runways.
