I don't think there is too much of a need to fight this. As far as I can see, KSM's 'confession' whether wholly accurate or not, adds to the weight of evidence supporting the idea that 9/11 was an inside job.
He has admitted responsibility for the Bali attack. But the then Indonesian President has said the Bali attack was probably an inside job, orchestrated by government agencies. Clearly then, KSM and his associates are hired guns. With bin Laden as an intermediary (with known CIA connections), KSM may not have known or cared who really hired him to plan and execute the attacks on 9/11 - he just did as he was paid and instructed to do. Even if he did know or suspected, any allegations he makes will never see the public light of day anyway, since his trial will be conducted in secret.
Bali tells us that KSM was not a religious fanatic but just another guy chasing the buck. This fits in nicely with the so-called 'fanatics' that are said to have spent their last hours preparing to meet a million virgins getting pissed-up in a strip joint.