First post here.
The only solution that I can think of to limit the chances of this happening again is to move the cockpit door back so that the toilet becomes part of the cockpit safe area and is only used by crew.
This way, none of the pilots will need to leave the cockpit area unless, they are on a wide body, long-haul flight where there is a relief pilot. Even then, the relieved pilot does not leave until such time the relief pilot is in his seat, which is normal procedure anyways. (I would think!)
On smaller planes, this is slightly more problematic because of the loss of the forward toilet, but this can be resolved by adding another toilet which will inevitably mean less rows and more squeezed PAX as the airlines will not like the idea of less sardines.