Trump reinstated Gallagher and his rank. He did not say he had to go back to the SEALs.
A staff review is in order for Gallagher. There still is some question of his suitability for any particular assignment that needs to be resolved, regardless of his pardon.
The SEALs are a very specialized unit. Not everyone qualifies. Very few, in fact, do. His actions may have made him unsuitable for SEAL duty. This review is to determine that.
After the Navy decided to review Gallagher SEAL position (entirely within their rights, even with the pardon), Trump made it clear to stop it and get back to work. The SecNav KNOWS this and has gone to the press to complain, versus simply contact the President and asking him in private.
THAT is the problem.