In the real-life military, there is a difference between being an officer of the line versus a specialized officer (such as medical or JAG--referred to in the Air Force as a "professional" officer).
http://en.wikipedia.org/wiki/Officer_of_the_line
One example of this is that in TNG, Dr. Crusher is a full commander, but with only one exception, she is not seen to take command, and if she does pull rank, it's normally restricted to a medical context under her powers as CMO.
By the description in the article, it might be that Sisko has sometimes been an officer of the line, and sometimes not--but even that article makes clear that sometimes the distinction is blurred.