For the sake of debate how about re-thinking your plan? Why use a Navy ship not suitable for this type of mission when there is a somewhat more suitable alternative already built? A cruise ship nearing end of life has the cabins needed and they would be interior. There would still be drawbacks but easier for remedies. The main issues would obviously be meeting needed ventilation and isolation standards including plumbing as well. That also means the sewage waste has to be pumped out at some point. Carrier would be same thing in that regard. So possibly a sealed tent within a cabin type of set up for isolation purposes might work as it does in a hospital. There is also fueling issues. A barge could refuel it. Any private relief org could do this. Another downside to any ship is doing away with medical waste it has to be burned.
Ships don't have boilers anymore? :p