You can absolutely define the ranks as you see fit, but bottom line it has to make sense if you want to seriously sell it. Organization should also follow suit, you shouldn't just make up whatever bullshit (and it's good that you didn't) to give a Mary Sue the authority to boss everyone around; that's what shit authors do when they're too lazy to research. Unfortunately if you keep refraining from actually touching on this stuff it's going to get harder and harder to write around as you develop the character, eventually you're going to have to define and and then you'll have to go back and review *everything* to make it kosher. Believe me, it's a pain in the ass.
For Moralez it sounds like his force is about a company of men so he'd be a captain or a major in army/marine ranks.You could go either way. (maybe justify army presence on a station because it stays in orbit so it's not moving and is thus army jurisdiction)
Science officers being completely fictional is... pretty much true. There's military researchers out there, but they're in military-run labs so treat them like a medical unit since they're pretty much parallel to that. We don't really have a need for soldier/sailor/marine-scientists in the Star Trek sense, but if they were needed they'd function exactly like a ship's medical officer. A good rule of thumb for anything is if it doesn't exist examine *why* it doesn't exist, and then look to existing structures for parallels. We don't have ship-to-ship combat in space and chances are we wouldn't except for very specific situations. Why? Laundry list of practicality reasons. What if we did? There's existing tactics and historical things (like shipboard marine detachment units) we can draw from.
My advice to you regarding all of this is figure it out now, develop a reference library, and go from there. Depending on how big you want this you can focus on just everything around Moralez and then a step further or fully define the UNN.