See the comments on Kalai's post from Peter Shor, where Kalai attempts to address this, and my reply to mantap on this thread where I try to give my poor understanding of the critique.
I'll just say the line between being unfairly critical and raising valid points seem to be a very thin one.
Especially when Peter Shore is disagreeing with the critique (and I agree with him).
Saying that a quantum computation does not qualify because it included (a short) classic computation does not seem a fundamentally fair criticism to me.
