You can still do these quests even after your factions "turn" is over and the portal has disappeared. You just have to fly to Arathi Highlands in the Eastern Kingdoms. The fastest way I've found to get there is the take the portal in the Great Seal to Orgrimmar, then in Org take the Twilight Highlands portal and just fly to Hammerfall, it's right above Twilight Highlands. Once you're there be careful as it's the other factions "turn" so you may want to turn war mode off.
Once you've completed the quests you may think it's impossible to turn them in as the turn in area is destroyed and the npcs are gone. But they are actually back on the Port of Zuldazar and will accept the turn in there.