The officer-heavy contingent is probably well in line with the tiny ship's top secret mission. A "normal" Archer
class scout might have a more balanced crew, but this one deals with issues requiring experts sworn to a high level of secrecy. Frankly, I think something similar was going on with the smallish USS Grissom
in ST3: the extremely sensitive Genesis affair was best handled by a small and unoffensive vessel, but a veteran officer of unusually high rank was stationed aboard that wussy little ship.
It's standard fare in this sort of drama, really: the humble mechanic is in secret a high-ranking intelligence officer, his Greaser's Mate 3rd Class a highly trained assassin, the ship's cook a scientific genius in disguise. Only, what happens inside the hull of a starship stays inside the hull of a starship, so the masquerade would not have to involve fake ranks and uniforms and false moustaches and other such nonsense...
For all we know, the Sagittarius
was an exceptional Archer
also in terms of the mission lengths and operations ranges she was supposed to cope with. A "normal" ship would do well with the dozen people aboard because the missions would be shorter and less demanding. Or alternately, there would be two dozen people aboard, again because the short missions would not yet make the accommodation unbearably cramped.
In terms of pseudo-realistic pseudo-military drama, I would have appreciated if the stories made it clearer the Sagittarius
was a much less capable vessel than a full starship. It would have been fascinating to see her rely heavily on outside sources of supplies, ammo and perhaps even fuel, there being a constant worry about making the next rendezvous with the Starfleet tender, purchasing the needed goods from the local merchants, or just plain reaching safety before the resources of the small ship were exhausted.