Cheney has a lesbian daughter which might be a consideration.
IIRC; The military will require its chaplains to perform marriage ceremonies resulting in married gay couples serving in the same unit. That might affect unit cohesion.
Pentagon: Military chaplains may perform same-sex marriages
http://www.freerepublic.com/focus/f-religion/2786310/posts
A Chaplan can refuse according to news report I heard.