Do you then think that the military in SGU should have submitted to Wray's authority? I expect the rules are somewhat different when you're out of touch with Earth, and can't have elections to vote someone into office... not enough candidates.
I liked that SGU had a lesbian character, but why did Wray have to be a power-hungry bitch? That's pandering to stereotypes if anything is. Now, if TJ had been lesbian, it would at least have been reasonably original.
No, because Wray was an employee of the military/government right? Only elected or those appointed/delegated by elected officials (PoTUS, VPoTUS, SECDEF) have constitutional authority over the military.
Employees fall into the chain of command. In today's military you can find deployable units with civilians assigned in non-combat roles. Many of these civilians are subject to deployment/ military authority as well. It is a condition of their employment.
That bit with Wray was just TPTB taking liberties with the ignorance of America on real military rules. At the time, if TJ had been lesbian-self admitted-she would have been processed for discharge. So much about TJ they got wrong. Mainly, her position. A medic. Enlisted people are medics. officers (as TJ was) are nurses, PA's and Doctors. Again, more playing up the ignorance.
You know our military has units where people sometimes get assigned when they are not fit to perform their duties for whatever reason. Officers and enlisted. These units are non-deployable as most of the people can't be trusted with responsibility or a weapon. I would say that every 'principle' military person in SGU would in reality be in one of those units and not sent to a high security, high importance base such as Icarus.
Some say BSG showed a lot of non professional non military type troops. But two things, their world just came to an end, some bad behavior is to be expected. Then, the Galactica was being decommissioned, most of her crew would have already been shipped out to other assignments. Galactica was mainly staffed with people nearing the end of their enlistments/commitments (such as Adama's retirement. Remember the new, "hot shot" viper squad that was being re-assigned to Caprica from Galactica? the one ho got shredded cause of the cylon virus?