It's not the exhaust that can't be submerged, it's the air intake. Those trucks are equipped with air intakes that come up by the top of the cab so they can drive through "most" water ways with out stalling out their trucks...

Now yes... the water was a bit high, but if you think about it they've been told "hey these things can handle it, you didn't buy the truck, just don't get water into the intake" and they're like "OH HELL YEAH LETS DO THIS ... wait, why does it feel like we're on a boat now and not in a truck???"

I'd do it. Chances are they didn't "hydro lock" the engine (which destroys the engine) but they probably just stalled the engine. The intake probably doesn't have enough pressure to suck that much water ALL the way into the engine with how long that snorkel kit (the adapter that makes the air intake come up above the roof is normally called a snorkel kit) is.

Here is a link to a snorkel kit for a jeep in you want to see what they look like.

http://www.jcwhitney.com/periscoop-off-road-snorkels-for-wrangler/p2011937.jcwx?TID=productads&gclid=CM32xOHM96oCFQfGKgodWCD3Cw

And engines are waterproofed so they can drive mostly submerged.  But when your truck tires start to float above the road, it's time to think of an amphibious vehicle.

Amphibious vehicles could have been used in this situation. The army has them.