The actual scriptSig, along with the redeem script and signatures, would be contained in a separate Merkle tree committed to elsewhere in the block, such as in the last output of the coinbase or the last output of the last transaction. Meanwhile, a hardfork variant would involve storing the signatures in another parallel Merkle tree and allowing users to validate everything else if they don't want to validate the signatures. Both proposals are related to Segregated Witness, a concept that apparently has not been written up much and is being worked on by SIPA and Gmaxwell. The soft-fork plan will be discussed at Scaling Bitcoin HK.