No, Hammond was in command of Homeland Security all through S8 and there's been no reason given (so far) as to why the post is now vacant for Jack to take over.
Hammond basically bunked off his job to insist he took command of the Prometheus when it was supposed to be heading for Atlantis in PU - a decision which had a lot of the Air Force brats in the fandom whinging that he would never (never, ever ever <G>) be allowed to get away with that.
So far as we know, that mission having been aborted by Vala's antics, he returned to his day job in Washington.
The Prometheus is generally - other than this aberration - under the command of Colonel Pendergast.
Hammond was also temporarily in command of Prometheus during the events of Lost City. It was after the defeat of Anubis's fleet that the President assigned him to Homeland Security.
Course, there is the Daedalus.
Prometheus's successor. Perhaps, having had a taste of excitement on Prometheus, Hammond's managed to wangle his way onto the command of her. But that's just speculation for now.
LabRat