Do you have an authoritative citation for this? By authoritative, I mean any actual scholarly work (refereed academic article, book authored by a degreed historian, etc.) that sets about estabilishing this phrase originating at that point in time. I sincerely doubt that this is the origin of the phrase: "Kill them all and let God sort them out." I am prepared to be further educated, but it does not ring true.
The book is mentioned on the web page for "Christianity Today" but I don't know what POV the web page comes from.
It was uttered by the Bishop commanding (!) a siege during the Albigensian Crusade, when confronted by one of his subordinate commanders who questioned the wisdom of torching an entire town that held orthodox believers as well as Cathars.