Data incomplete, but it looks to me that the best way to do it is to pick long missions, 4 or 8 hours. Then track your Fatigue % with this mod. When the Fatigue gets to about 40-50%, let your Agent be idle for about 4 hours and they will be mostly recovered and can be sent on another few 4/8 hour missions. This cooldown is roughly half of what you have to wait if you become incapacitated.
Edit;
Here are my conclusions from testing and recording this system over the past couple days. (Quoted from my post in that mod thread).