Perhaps. If the terrorists do it the exact same way as on 9/11. But suppose they fill the cabin with a debilitating gas? Suppose their plan is to draw out the Air Marshall with deliberate provocations and then quickly overwhelm him with numbers and grab his weapon? And remember, with the reinforced cockpit doors, all the terrorists need to do now is take control of the cockpit and the passengers can fight all they want out in the cabin.
I would think with the reinforced doors and the probablity that the Pilots are carrying, there would be little chance of them taking the cockpit.