Good points. His position must have been tenuous anyway as it was a requirement of Cambridge that all Fellows become ordained Anglican priests. Newton only avoided this by special exemption from Charles II and it is not likely that he could afford to be exposed as breaking other regulations. Maybe this is part of the reason he was so reluctant to publish, he may have wondered if his physical reasoning could be construed as somehow against the prevailing religious beliefs of the time, especially when you see the approbation Newton's intellectual predecessor Galileo suffered for his new physics.