Anonymous Blitz Assassinations
Here are 3 ways to kill Checco quickly without being detected.
Dive underneath the canal grate to cross the city walls quickly. Transition to fast walk as you pass through the group of people standing by the fast travel station. You remain blended for several seconds after you emerge from this group, which gives you time to approach Checco unnoticed.
You can also go over the city walls to avoid the guard post at the drawbridge. In this example, I run around the fast travel station to approach Checco from behind.
You can use smoke bombs to stay undetected. If you watch carefully, you'll see that the game doesn't have enough time to spawn the civilians next to the fast travel station. With no civilians to blend with, you can only go around the fast travel station to stay undetected. I play on PS3, but the same effect can be seen on XBox.
The Tripwire
All of the remaining clips in this video start off the same way. Get Checco's attention so that he starts running, but don't chase after him (yet). Take a shortcut across the canal. Since your pursuers cannot swim, you will usually become Anonymous a short while after reaching the other side. Just be sure to keep your distance from Checco at 60 m or fewer, otherwise the mission ends with desynchronization.
Checco is running to a viewpoint tower along a fixed route. Aim the gun across Checco's flight path and wait for him to run across your shot. Despite appearances, this isn't really a tripwire, of course. Fire the gun at just the right time to make the kill.
The Ultimate Sniper
Ezio can't move while he is aiming the hidden gun. This immobility ordinarily limits how far you can be from your target, but in this case, your target is running away from you...
You need to be within 15 m to lock onto a target. Once locked on, you can maintain that lock if you remain within 30 m. If you start to aim the pistol at your target while you are locked on, you will be able to maintain your aim as long as nothing obstructs the path of the bullet, regardless of how far the target travels from you. You desynchronize if Checco is more than 60 m away, so that means that you can potentially shoot him from as far as 60 m away.
In the first clip, Checco runs to the viewpoint tower and comes to a full stop when he gets there. If you shoot from this specific location, you'll be at a distance of exactly 60 m. After you shoot, however, Checco is knocked away from you as he falls to the ground. That means you return from the Memory Corridor dialog more than 60 m from Checco, which desynchronizes you. The assassination mission then reloads from the last checkpoint as if the assassination never occurred. If you wish to avoid this, shoot him at a distance of 56 m instead. In this case, the story will progress when you return from Memory Corridor dialog.
My personal preference is to use a tower for the sniper shot. Due to all the climbing to reach the tower, you'll need to maximize you lead over Checco at first, yet take care not to exceed the 60-m limit. When you reach the top of the tower, you'll need to quickly lock on to Checco, as there are only a few moments where he will be within range to do so. Be sure to fire the shot before Checco runs more than 60 m away; timing is an important issue if you want to maximize the distance of the shot.
Air Assassinations
Instead of using the hidden gun, you can air assassinate from the tower if you wish. You can also hide in the nearby haystack and wait for Checco to pass by. Hold down the high profile button and press attack when you see "Assassinate" appear in the control HUD. Ezio will jump out of the haystack and perform a nice long-range air-assassination. If you miss this opportunity, you can follow Checco to the viewpoint tower at the end of the chase. Sneak behind the building. An archer will spot you as you approach. Wait for him to jump down; then kill him. Use a throwing knife to kill the other archer, and wait for the guards to cool down from inspecting the dead body. You will not be able to lock onto Checco from the top of the tower, so you'll need to lock onto him before you climb all the way up.
By Horse
The goal is to chase down Checco by horse, dismount over the horse, and then assassinate him with the hidden blade. Both the steering of the horse and the direction of dismount are controlled by the left stick, so you have to be careful about how you execute this. Another complication is that you have to change weapons to the hidden blade after dismounting since the default weapon after a dismount is the sword. I use my left index finger to press up on the D-pad on the PS3 controller so that my left thumb can remain on the left control stick.
Waypoint Separation
Watch this video if you are unfamiliar with Waypoint Separation:
http://www.youtube.com/watch?v=Qo2lTyCD3GM
Grab Checco and drag him so far from his next waypoint that it is no longer modeled in the game. Since he has nowhere to run to, you can let go of Checco (by waiting for him to push you away), and he won't move. Kill him as you please. He doesn't have much health while he is in "flight" mode. A single punch to the back can kill him. So does a single bullet
Good stuff. Lots of options with Checco. He's a bitch to fight unarmed at the final waypoint too.
Have you tried dragging him over to the water and throwing him in?