Well, historically... (since that seems to be the rage - lol)

... spearing the enemy in the back when they turned to run was the fun part, and until the age of chivalry, such an opportunity was rarely passed up... even then, it was pretty standard procedure... very few commanders would allow an enemy to run off to trouble them another day. Rarely indeed would a general be suitably impressed by the others fortitude, honor, etc to allow them to quit the field in safety. Occasionally, to avoid over-extension, this might be done - but by and large, the loss of the battle by one side marked the begginings of a "great slaughter"...

If you're concerned about fairness to the computer, there's a simple solution. After a loss, disband any troops which you feel would not have been able to escape. That's easily figured out. If they had light cavalry - get rid of most or all of your infantry. If some of your heavy cavalry were close to that light cavalry - get rid of them too, etc, etc. If they were a bunch of plodding phalanxes... keep your men.