The Champion's Early Deaths
http://www.youtube.com/watch?v=v81JVJdqa3c
The Champion from the master assassin mission can be killed early both times he appears in the game.
The Champion Part 1
The Champion appears at the last checkpoint in this mission to fight your recruit. Meanwhile you have to chase after a printer who gets attacked by two guards. After the guards appear you no longer have a distance restriction on the printer. When you kill both guards the recruit sits by a wall and the Champion walks away to a certain spot. It's strange that the game developers didn't make him disappear instead. One time he did seem to vanish in thin air, so maybe that's what they were planning, and it might just be glitched. The Champion has the basic ai of a guard, but doesn't take any damage. Drowning him is an effective way of killing him, though.
The Champion Part 2
After fighting groups of guards the Champion appears to hold a herald hostage. Here's how to prevent that. Plant a tripwire splinter bomb in the spot where he will come. You need to watch out for other characters who could activate the bomb. It's best to plant it when the fighting is nearly over. After the target appears he steps on it, killing him instantly. The scene can't end now, and you don't have the option to skip the cinematic.
Getting Around the Scripting of the Mission
This is something I found and decided to include in the video. The target is holding the herald hostage. Since you are always in his line of sight it is impossible to kill him without desynchronizing. This is why you have to call your assassin recruit on him. However... To get around this you have to call the recruit while starting to perform an air assassination. Start by climbing the wall of the building to the right. Climb from the lower side and go around the corner (you can't climb from the left side because of an invisible barrier). Then jump to the beam. You are now in the area where you can call the recruit. If you air assassinate without calling the recruit you desynchronize. And since the recruit kills the target pretty fast after calling him you have to already been performing the air assassination. So press the attack button and lock onto the target in midair. If the timing is right you will beat your assassin to the target. It's obvious you weren't supposed to be able to kill the target yourself by the memory corridor scene with the recruit holding the target in his arms and Ezio standing there.