The frustrating thing about this is that as soon as the method that the terrorists used to take over the planes in 9/11 was understood, the take-over-the-cockpit scenario became much harder, because now you have to defend yourself from all the passengers as well as the crew. There was no downside to adding the door security, but it was superfluous, and now we can see that it has a serious downside.
I think the problem here is thinking in terms of absolutes. What was needed to address the 9/11 scenario was a change to the balance of power, not a perfectly secure cockpit. Having a lockout that prevents crew from accessing the cockpit is too much security, because while it mitigates one risk, it creates another risk, and the second risk isn't particularly less likely than the first.