Is the disease caused by the spell contagion considered a supernatural/magical disease? It could be argued that the infection method is magical, but the disease itself is not magical.
The Contagion spell lets you infect a target with the following diseases:
Blinding sickness
Cackle fever
Filth fever
Mindfire
Red ache
Shakes
Slimy doom
None of which are described as being supernatural diseases in the SRD. As such, I believe that while the method of infliction is magical, the disease is very much a normal disease (as much as "Slimy doom" can be "normal" )