They should change mission timers to be purely based on time spent in ingame, that way, they can now reduce the time to complete missions, and offers higher rewards for tighter time to complete...
So now we can all relatively safely, log out in the middle of a mission run, go on with our lives, and then login a few days later and pick up where we left off...
Of course this can create issues with missions that requires certain system states etc, but already the game have been happily to give out a mission that requires an active war, and then the system update, and then war is in a cease state and you can no longer complete the misssion, and you can still pick up mission that require the war to be active... so we do not need to worry to much about it.