The Hidden Blade Assassin's Creed in Depth

Early Death
When you first start chasing after Charles Vane he appears at a view point. The mission is scripted to make him escape before reaching him, however they overlooked the fact that you still have a throwing knife available. by climbing to the spot shown in the video you can knife him without activating the next checkpoint. Killing him has no effect on the mission, and you continue as usual.

Early Death 2.0
During part when Charles shoots from a log you can also knife him, causing him to disappear (counts as a kill in stats) and activating the next checkpoint.

Use of Poison
Normally you can't use poison with the blowpipe gone during the mission and no ammo. However after crafting a dart you can counter tool with it.

Blitz
Another time the throwing knife comes in handy. To avoid his gunshot run behind a ruined wall and proceed to a part of the building you can climb up to (ironically located by a scaffold the target collapses to prevent you from getting up there). When you get in range knife him.