Just like the Comfort, the Mercy is set up for trauma patients, battlefield wounded, and not infectious disease patients, which have to be physically separated by greater distances, partitions, and require a different level of PPE and biosecurity.
In addition, disinfecting a ship is far more difficult than disinfecting land based facilities.
For that reason, the hospital ships, so often used to provide relief in natural disasters (often trauma, seldom communicable disease) were provided to lift the trauma load from the municipalities to which they were assigned.
It really isn't the Navy's fault that shelter in place orders and work from home policies have so severely cut the number of gunshot wounds and accident victims, the more usual ER fare.