Re: bitsofproof supernode vulnerability: block chain split / node isolation

I don't think so. Check https://en.bitcoin.it/w/images/en/7/70/Bitcoin_OpCheckSig_InDetail.png

The script scriptSig is completely removed from the transaction when the hash is performed. It's replaced by a part of the previous scriptPubKey.

Yes, but the value part of the TxOut structure would be different isn't it ? That is part of the hash.

IMHO, No.
The only difference between TxA and TxB is the signature and the public key, and both are removed before the hash is calculated.