Original storyboard ending
I've got the Special Edition DVD and it has storyboards of the action sequences. It is interesting to note that in the storyboard for the final chase, the drawings show Popeye Doyle with a machine gun. He is chasing Charnier across the harbour and just as Charnier climbs over a fence, Doyle shoots him and he falls into the water.
This would have been a more action-packed ending, but I'm glad they changed it to a suspenseful chase where Doyle finally dispatches Charnier with a .38.