Fraternization is actually about officers and enlisted--with John and members of his team, it'd be about "unprofessional relationships" (3rd para of AF article) since none of them are enlisted. Jack/Sam wouldn't have fallen under fraternization, I think, since technically that applies to officers and enlisted and they're both officers.
To answer your question, yeah, I think there would still be a problem with John sleeping with a teammate.
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Fraternization is actually about officers and enlisted--with John and members of his team, it'd be about "unprofessional relationships" (3rd para of AF article) since none of them are enlisted. Jack/Sam wouldn't have fallen under fraternization, I think, since technically that applies to officers and enlisted and they're both officers.
To answer your question, yeah, I think there would still be a problem with John sleeping with a teammate.