Pilots are trained to keep their cool in an emergency. Failure to keep your cool is a quick way to die. Here is Rich Husband's profile:

During his tenure in the Air Force, Husband logged more than 3,800 hours of flight time in more than 40 different types of aircraft and served as a flight instructor and a test pilot. He also earned a master's degree in mechanical engineering in 1990 from California State University, Fresno.

Here's William McCool's profile

In 1986, McCool began his flying career with the Navy. He flew 24 different aircraft, including the EA-6B Prowler, and had more than 400 carrier landings. He became a test pilot in 1992. The pilot served on two aircraft carriers, the USS Coral Sea and the USS Enterprise, and had more than 2,800 hours of flight time.

We may never know how aware the pilots were of the damage during reentry. It seems likely they knew something was seriously wrong, but they may have been so busy handling the problem to give it a lot of thought.