Problem with any morale system in 3.X is that enemies are worth far too much XP NOT to fight to the last HP. Previous editions had lower XP awards per creature and generally higher numbers of creatures, so "Free XP" of a few foes fleeing while it could still provide a chance of consuming some resources was not as bad. With 3E, almost every creature's actions is literally worth 100's of XP. Throwing those actions away on running is giving the players free XP.
To me, if you killed the monster(s), or they run away, the players get the same XP for "winning" the encounter.
So, sometimes, the players in my last 3.5E campaign would get XP for defeating a foe multiple times. They had an re-occurring foe that they fought at level 3, level 4, level 9, level 12 and level 16 for the last time...each time, they got XP for fighting her & her allies.