Just after Carter reveals that there was nothing left on the planet but the miles-deep stack of Replicator blocks and the building in front of them, they go down stairs that are full of spider webs.
While Jack's hologram talks to General Hammond in the control room the Stargate is visible and the iris is open. As the purpose of the iris is to protect against intrusion, it should be closed at all times; opened only after confirmation of a gate code.
Thor states that they sent out an instruction to all replicators to "come forth" and gather on Hala. If this is the case, there is no "replicator-dominated space" any more for the Prometheus to fly through. There is also no reason for the Asgard to have abandoned their entire galaxy.