I always thought that the "disease" SCP-049 refers to was life itself. Either that, or something like sin or committed crimes.
Yeah, at first I although thought that the disease was life, because, you know, the cured are ZOMBIES. However, it didn't make sense when I read the addendum with the doctor, because I'm pretty sure that guy was alive.
049 does say to the doctor that he doesn't detect the disease and THEREFORE he assumes he is a doctor. I think this is significant. I doubt a Class D is going to be "pure" in 049's eyes. Not that being a doctor automatically makes one pure or vice versa, but if being pure makes 049 assume a person is in the medical field, then that must be significant. Perhaps its related to its perception of cleanliness? I wonder how SCP-049 would react to SCP-106.......
I don't think you job would have anything to do with you having a disease. Also, if it was so, then wouldn't all the doctors be considered clean? The thing is, we don't know what the disease is (why didn't the guy ask him, I don't know) but we know that there is a small percentage of people that don't have it. Which as said before, could be implemented in the game.
The plague doctor is one of my favorite SCPs, which is why I think he should play a more important role, and yeah, he should have a different beak model.