The Navy needs to be smart about this. First, if I was enlisted I'd look at my enlistment/re-enlistment contract. Doubt there's any provision to repay those funds under the conditions the Navy has now levied. Second, this is a horrible retention tool. You have to ask how many military people, not just SEALS, will remain in the service after being forced to take a vaccination they are deeply skeptical about. Costs a LOT to train a SEAL, a Korean linguist, a pilot. Those close to retirement may retire at the first second possible, depriving the military of their experience when it can often do the most good. Others will just leave at the end of their obligated service. In any event, the service loses out on experience and must spend that recruitment and training money all over again.
And morale has already gone down in the military over this stuff. Most military people have been vaccinated, some quite willingly. But the heavy-handed tactics being used now don't go over well with an entirely all-volunteer force. Troops with low morale can act it out in many ways. Some will leave, some will no longer go the extra mile to get things done unless they are helping their buddies, some will no longer attend any voluntary off-duty things if upper echelons are present.