In TNG era all station commanders were commanders. So, it tracked with what people would have seen previously. It's internally consistent, and the fact that external factors might make it "look bad" doesn't mean it should change.
He got his promotion. DS9 was established as a lesser assignment, that was essentially viewed as "career suicide" at the beginning of the show. So, giving it to a captain would appear like his superiors had no confidence in a higher ranking officer. So, it looks bad either way.
I found it consistent with what TNG had established, which I thought was supposed to be a plus. Now, it's not...