It is easy to check whether a similar mutated transaction got on the chain or not.

Surely, with out even needing to modify the bitcoin client or protocol an easy solution would have been to monitor the inputs of a transaction when a user withdraws.

i repeat: it is easy to check. just dont use txid for comparison instead use input and outputs (and i dont mean addresses).

b) detect the modified version of the tx (when it scans blocks for new txs anyways) and modify the client's records so the tx shows the proper confirmations and the new modified tx hash?