IMHO a full face mask or "airtight" seal to the cockpit is a little much. Most infectious diseases are transmitted through aerosolized droplets (coughing, sneezing e.g.), touching of infected persons skin, or sexually.
Considering that the pilot does not necessary have to touch the patient - or even talk to - the risk of infection in a controlled environment it rather slim. So if the patient and personnel are wearing a simple mask, gloves and coverall (incl. hood and maybe safety googles when caring for the patient) and follow simple precautions, you should be fine.