^That's my take on it as well. All of the stuff in the Taurus Reach was supposed to be one of Starfleet's biggest top secret operations at that time, so IMO it makes sense that they might crew the ships with some higher ranked personnel than normal.
Ok, that makes sense. Ranking officers with appropriate clearance would make sense.
That, and Starfleet doesn't do enlisted ranks very well. Most of the stuff we see officers doing would be handled by enlisted personnel.
I could be imagining this, but in Mr Roddenberry's creation of Star Trek, did he not have that everyone would go through the Academy and therefore be an officer?
In one of the tech specs books (for Constitution, Saladin, Hermes and Ptolemy classes) it gives department breakdowns and has no enlisted ranks, only Ensign and above.
Commander Austin Harris, First Officer, Deep Space Nine (by FltCpt. Bossco)
8.01 - Darkest Before Dawn
(Chapter 8 added, 12/09/2015)