There is an old saying. "Everything is fair in Love and War." But the truth was, it was fair as long as it was above the bottom line set up by the Churches. The moment you break past it, the whole world can turn into your enemy.
Specifically the Church of Plagues, who might use and control plagues and diseases, but there was no one in this world that hated plagues more than them. They were contradictions themselves and hence made fun of among certain sects of beliefs.
But none dare to show it in front of the Church of Plagues. For they know the horror the Church of Plagues was capable of harnessing.
This was one of the reasons why Cynark, through all they have done in history, never dared to weaponize any diseases to their advantage. It was not worth turning a Neutral Party like The Plague Church into the enemy.
However if one were to use plagues during war, they have to have a way to cast aside any responsibility.