I don't see the issue. It's a sports car; sports cars are low. The Model S is definitely not the lowest around town. Some quick google results on stock ground clearance: (not sure if all are 100% accurate or measured to the air dam or what)
Prius is 5.5"
Volt is 3.7"
Porsche 928 is 4.5"
'14 C7 Z51 is 3.25"
BRZ 4.9"
etc.
The reality of the situation is that road debris is not a uniform size. Yes, the Model S is low, especially with the air suspension at freeway speeds, but there are enough other vehicles on the road with low ground clearances that they should experience damage from debris as well. Even if you boosted your Tesla up to 7" of ground clearance, if you hit a tall metal piece in the road, it's going to have the same effect either way.
I think we'll just have to get used to the "car bqq" jokes. The current situation is that if you run over something serious on the road, your Tesla may catch on fire and burn down. In all my years of driving, I've never personally heard of or seen a gas-powered car running something over and catching on fire. I'm sure the statistics say otherwise, but I have yet to hear somebody say "I ran over a big piece of metal on the highway and my car ignited and got totaled!" It is apparently a risk of driving a Tesla. It is also good to know that the safety systems continued to work and that everyone got out okay. I'd still rather take a Tesla than any other car on the road in light of the recent events.