In Kabbalah symbolism, the left side is the Arm of Shields, it's the strength of your past, it's the strength of your heritage. It's what you draw upon. And on your right is the Arm of Swords, the arm of attack, the thing you use to create your future. So basically Shinji has lost the past, it's like all he has is instinct, destructive power. This is why he reacts with such horror: he's (subconsciously) seeing the fact that he has lost everything that has existed before."