The crisis of faith was a problem, but it was also an opportunity. At this time, the Vatican was so preoccupied with its own troubles that it created favorable conditions for the government to intervene in the Church's internal affairs.
If the government had the right to punish clergy, then from now on, the Church could only submit.
Otherwise, they would be investigated for violations of canon law. It's not outlandish to say that out of ten clergy members, seven or eight could be found in violation without any issue whatsoever.
The remaining two or three shouldn't be complacent either. If they haven't yet violated canon law, it's only temporary or simply hasn't been discovered. As long as the government wishes, problems can be found sooner or later.
It wasn't just Franz who kicked the Church when it was down; the crisis of faith significantly reduced the Church's status in the eyes of the people, and governments across Europe unanimously cut back the Church's privileges.
