Originally Posted by Ksheep
I'd say easiest thing to do is A) Fort save, with a low enough DC that level 1 commoners will be fairly susceptible, while higher level PCs have a much lower chance of getting infected, or B) Incubation period of several days, during which time you can attempt to cure it via spells or medicine (although medicines will probably be highly experimental and my have some side effects).
Hitting that sweet spot can be tricky, especially for classes with low base fortitude saves or that normally like to pump stats other than Constitution. What I might do is have a character make several fortitude checks over the course of several in-game days, with each failure advancing the disease a little more.
Essentially, it's leaning on the law of averages: on any one roll the commoner might get a 20 and the PC a 1, but on several rolls together the PC is more likely to shrug off the effects more often, and therefor delay succumbing to the disease longer.
I've never tried to parse out all the implications of magic vs viral zombies in the same setting; I'd be very interested in hearing how all this plays out once you are done with the campaign.