Perhaps she found the inconsistencies of the left impervious to the reason she was forced to abandon. Under the purely ecclesiastical discipline no temporal punishment could be inflicted on the obstinate heretic, . . I thought the author hinted it was all the fault of the local governments. Then I read on.
Cruelty only comes in where the punishment exceeds the requirements of the case.
The author was careless enough not to say. If the former or middle, it would have been an attempt to justify. If the latter, then it changes much. That would not be justification of physical assaults upon heretics.