Again, keep in mind that the Chidori is like a knife. It makes a direct, linear impact. The impact is great enough to pierce through Gaara's armor, but all that shows is that it is able to pierce something as soft as skin. Consider the case of the water tower on top of the hospital. The Chidori simply made a straight hole of equal width to Sasuke's arm, showing that the Chidori is nothing more then a very hard stab. At that point, no matter how hard Sasuke hit Naruto with it, it could only do a limited amount of damage. Imagine being stabbed once with a knife. The knife, no matter how hard it is stabbed into you, will only go in as far as the blade, and will only create a wound as wide as the blade. Sasuke did use the Chidori, and struck Naruto with it. But because of the mechanics of the Chidori itself, it could not have killed him unless it hit a vital point, which it did not as a result or Naruto moving slightly to the right. If the Chidori made an explosion or a burst, things would have been different, but it does not.
Here is my craptastic diagram:

Now, if we were talking about the Rasengan, it would be a different situation entirely, and an impact like that to the chest of Sasuke would definately killed, if not having severely maimed him. The Rasengan does release a burst. Again, review the water tower hit by Naruto on top of the hospital.
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