The Vatican position (as offered here) is that why the act (abortion) that gave the cells for the making of the vaccine is wrong the use of the vaccine is not prohibited.
I was in the middle of writing a post for this at CGBlog.org (post: The Coast Guard, The Church, Right, and Wrong when I got the new post eMail from here. Thank you FlynnPatrick for pointing our that address to the catholic news piece, it made my writing easier.
Though I think this would be a hard pill to swallow at the top level, they (HQ) have an obligation to the public, and the rest of the service members of ensuring we remain healthy. We can't do our job, if we can't do our job.
Simple solution is to use the US unapproved European vaccine. If both vaccines are refused, then a limited duty comment should be entered in his personnel jacket prohibiting any duty in a Hepititis risky area. Working at a stateside telecommunication command the risk is non-existant. Of course this will result in a 20 yr career. A senior offficer is expected to unrestrictive movement.
Using unapproved FDA vaccines is not prohibitive, otherwise they will never get approved.
I bet the CG will lose this case. They should use the time to prepare an alternative vaccine.