The DOJ threat of criminal prosecution only becomes functional when the president becomes a private person, at which point the president no longer has the ability to act in an official capacity anyway.
As for SEAL Team 6, they have a "duty to disobey" unlawful orders[1]-- which every member of the team probably knows off the top of their heads-- and which is a much more effective real-time check on a president's authority.
[1] https://www.findlaw.com/legalblogs/law-and-life/what-is-a-mi...