Mordyval,
Isildur said this:
"Whether the reason for this threat can be considered evil is irrelevent, we seek to prevent it."
This is saying that whether Chaos is evil, or even if it is not, the Church perceives it as harming the "...part of existance in which we mortals reside."
By this I presume he means the material plane.
He is informing everyone that the Church now perceives Chaos this way, and that the Church will oppose it, not nessessarily because it is evil, but simply because it poses a threat.
Caled Tiercel

Penned by my hand on the 11th of Glacian, in the year 250 AF.