That's a solid theory and makes sense. There are a few loopholes though:
1. I am solidly sure that 049 only regards a few people with the Pestilence. If the others also have the Pestilence, or mortality, in your theory, why isn't he trying to kill everyone?
2. He doesn't kill other "living" anomalies either.
3. He used to operate on the corpses that were "cured". Why? Because there'd be traces of the Pestilence. For research. However, corpses are definitely completely cured from the disease of living.