Bajorans wear a Lt. Col. pin in season 2 that is different from Kira's Col. pin in Season 7. Kira is never referred to as a Lt. Col., just a Col. All signs point to Kira receiving a 2 rank promotion to full Colonel.
Keep in mind Kira's promotion occurred while Sisko was on indefinite leave, so it may have made sense for the Bajoran government to push for her higher rank to keep a Bajoran presence on the station, or that Kira was the only person that Bajor and Starfleet agreed could hold the position. Given that Sisko held higher responsibilities when he returned (and the writers had wanted to promote him to Admiral even in Season 6), it makes sense that the two could hold equivalent ranks, with Sisko being more involved in the war and Kira more involved in managing the station. After all, the Enterprise-A had 3 Captains on it in the later TOS movies.
Why Kira was only given a Starfleet commission at Commander is unknown, but it's simply possible that they didn't want to confuse fans with two "Captains" on the same show (according to the script, Kira was originally supposed to be given a Lt. Com.'s commission, which complicates things even further!)