The Daedra on the wall are always there, they should not impact at all on the quest. Make sure you have killed ALL the creatures in the relevant area before you get the request to go through the chapel to open the gate. If one is hidden and left alive you won't get the update. The Imp Legion types don't show until AFTER you have the quest to open the gate. If you have killed everything and the Captsin still does not ask you to speak to Berich Inian you can advance the quest via the console. Hint to keep BE alive, when he leads you into the crypt run straight through. He will stay fighting Daedra in the crypt. When you and your legion comrades have cleared the way, return to him and then follow him.