Anybody with a disease that would warrant forbidding them from getting on an airplane is presumably being legally forcibly isolated/quarantined anyway. If not, then I see no problem allowing them on the airplane; the common flu is a "highly airborne-communicable disease", but we certainly don't stop people with the sniffles from flying.
I think the idea there is that those with diseases like drug-resistant tuberculosis should be prevented from flying because of the risk it presents to other passengers. It's really a matter of degree: While both diseases can kill, and certainly influenza is far more virulent, you're less willing to take a risk with a diseases that's difficult to treat (if treatment is even successful) and is infectious.
I'd think the same thing would occur (or I'd hope so anyway) if a form of influenza popped up that was highly fatal and contagious.
