So: a given organization claims to be operating on behalf of a particular god.

In fact, the organization claims to be speaking for that god. They claim that said god actually works through them.

Then it becomes clear that said organization has actually been operating in its own self-interest and, in so doing, has not only permitted, but has systematically protected—and, in protecting, promoted—the most profoundly immoral and destructive behaviors among its functionaries.

Now, this is just me asking, a nobody from nowhere. But really, I have to wonder.

If you had ever taken seriously this organization's claims to be acting on behalf of its god....

Would you not seriously wonder if this organization had ever really been acting for a god?

Would you not seriously wonder how any god could countenance such a thing?

Would you not seriously wonder if such a god even existed?