Depending on the service, though, scientists don't have that kind of authority, even given the rank. Really, the medical career fields in the U.S. military are a bit of a joke. Not much on the rank n' file kind of thing. Scientists? Even worse. There's a hierarchy, of course (hence, the ranks), but it's not like it is for regular line officers. In the Navy, they have Limited Duty Officers and Warrants to who that kind of specialist work. The AF's officers who are also scientists are not in command of squadrons or anything like that, as well.
Now, that having been said, I concede your point. He could have been conscripted (and, anyway, I'm just providing the perspective from a U.S. and UK military paradigm, which Starfleet is largely based on, but they likely have some operational differences). But, contextually, it seems like he was working on the spore drive before the war and didn't appreciate Starfleet putting it on a ship of the line. But that kind of resource allocation couldn't've come from anyone else other than the government; hence, Starfleet. It's too radical, probably too expensive, and too experimental for something the private sector would've been doing. And its very secrecy--the fact we've never heard of it until now--seems to militate against a private sector approach. Hence, back to Starfleet.
I just think it makes more sense to say he was already in Starfleet but he was--like most of the personnel of the day--of the mind that Starfleet was more of the exploratory mission-set than the military one...and was quickly disabused of that notion by his CO.
But, again, I'm open to reinterpretation if more evidence comes to light.
