Crozier certainly knows that the mission comes first. And in his heartfelt letter, he acknowledged that if we were in a war, he would simply do the best he could, hope most of the infected had only mild symptoms, and go to the fight weakened but hopefully operational. But the USS Theodore Roosevelt was not headed to war, a circumstance in which the health of the force has to come first. In this case, the extraordinary choice was to evacuate the crew (all but the 10% needed to run the reactor and disinfect the ship) and keep the ship parked in Guam for at least two weeks.
Having felt many times the surge of pride that goes with leading a ship into a deployment, I cannot imagine how wrenching the feeling of signing that letter must have been for the captain. But he made the right choice, and the Navy will back him up – although the exact number of sailors leaving the ship is still under scrutiny. The challenge for the Navy will be rapidly identifying and isolating infected sailors, as well as making up for the gap in carrier coverage.