You can disable fatigue altogether by editing your preferences.txt file.
Find where it says:
FATIGUE:TRUE

and change it to False.

Other than that, the AI is doomed to more or less ignore fatigue considerations, once again reminding you how poor it is. Many close battles I've won by keeping some of my troops rested whilst the AI troops commit suicide by chasing after routers for no reason whatsoever, before returning to challenge my fresh soldiers and then falling over their own feet before even a sword has been swung.