The only answer is going to be to make the cockpit non accessible from the cabin. This will take time to implement and will not be nearly as expensive as the other interim solutions which include skymarshals. Not only do you have to pay the skymarshals for each and every departure, but you lose 2-3 seats per flight, far more than the space required for an extra lav on the long range planes, and the regional jets can do without a crew lav. I flew Metroliners for years and they never had a lav anywhere in the cabin, eventhough some flights were as much as 2 hours long.
Things are gonna change, and now that an aircraft is recognized as a weapon there is no going back to the way it was.
Wino