Of course, when Vaan thought they were fucked in passing, he meant the human countries that had yet to fall under his control. That said, the situation in the Great Ratholos Empire wasn't completely unsalvageable.
After all, he was here.
The only difference was that there would be a lot more deaths compared to his original plan.
However, there was no other way around it. Devil beliefs had taken root in the empire and propagated to a threatening size like cancer. The only way to save the empire was to remove all the cancer cells from the main body.
That said, if one wanted to do that, one had to identify all the cancer cells first, which was also the most tricky problem to tackle.
After all, a contaminated body was easy to identify, but a poisoned mind was difficult to determine.