Right, but I'm talking about two separate units where a particular mission gives one authority over another. Rank doesn't have to match up in those situations. So if Starfleet was run similarly, a starbase commander wouldn't have to outrank the captains of the starships it services.
Now what you're talking about definitely makes sense for Sisko himself if we assume that a few things happened off-camera. For all we know, DS9's CO position was originally pegged at a rank of Commander and then upgraded in significance somewhere between the discovery of the wormhole and shortly after the Odyssey incident. However, assuming Starfleet knew they'd be promoting Sisko fairly soon, there was no need to shuffle personnel around. It's probably unlikely though that, for the rest of DS9's serviceable lifespan, it would ever end up in the hands of a Commander.