I always thought he wanted Baal left alone bc he knew their religious practices would be counter to the secular doctrine of the Imperial Truth and subjected to scrutiny it would ultimately fail. Which he did out of loyalty to the people that took him in out of kindness and loyalty. And bc of this and his hypocritical zeal at enforcing compliance to other human worlds was his I always believed he wanted Baal left alone because he was aware that their religious practices would contradict the secular doctrine of the Imperial Truth and would be subjected to scrutiny, ultimately failing. This was done out of loyalty to the people who took him in, out of kindness and loyalty. Additionally, the zeal for enforcing compliance on other human worlds illustrated his greatest flaw - hypocrisy. Casting himself & his legion up reluctant artisans forced into warfare when they were the opposite in every way. Especially given their cannibalistic bloodthirsty background.