The Hidden Blade Assassin's Creed in Depth

So invisible assassinations (starting a memory corridor scene right before an assassination mission by assassinating a character while he is despawning) are also possible for Al Mualim and Robert de Sable.

Al Mualim Invisible Assassination
The civilians inside the Masyaf fortress disappear when the cutscene in the garden starts. So throw one of them there (don't throw him more than a few times or you'll take out all his health). After the memory corridor scene the game glitches with Altair since he is teleported to the usual spot after the memory corridor, but still affected by the scene started by entering the place. You then hear the dialogue with the dying Al Mualim, "I applied my heart to know wisdom...", but the regular cutscene also starts regardless. After the scene you are unable to perform any high profile actions and can't progress any farther into the game, not to mention the camera zooms out.

Robert de Sable Invisible Assassination
With Robert you use a guard for the assassination. When fighting the last wave of guards in Arsuf kill the high level ones first and the last remaining few will abandon the fight. The memory wall won't disappear until you kill a certain amount (you'll know when because the game will lag for a brief moment). The scene starts when you're about fifteen meters away, so at sixteen meters high profile kill the guard to start the memory corridor scene.
Afterward the scenes before and after the memory corridor are merged together for a while, but eventually sort themselves out. Since the memory corridor has already happened, you automatically progress through the game after the scenes.