Whenever you perform an action, brain activity ensues. When Kirito was paralyzed, he was basically trying to fight back against the system programming through will power alone, and after that his arm was cut - btw, you don't feel pain in SAO, his moaning when Kuradeel stabbed him was due to pure fear, as anyone should feel - and killing Kuradeel right after, well, to be honest, I would black out if he was me, and he's just a teenager.
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