So anyone using Bitcoin and needing an accounting system, has to watch addresses.
You talk as if Bitcoin Core is the only implementation for full node client. While i wish Bitcoin Core have address index, there are alternatives such as running Electrum server or local blockexplorer.
It could be optional just like txindex.
Unlike RBF, the actual malleability doesn't need access to the private keys. Anyone could just take literary any transaction and perform certain acts like inserting any garbage at the beginning of signature script and create unlimited number of still-valid transactions.
That doesn't justify the incompetence of those who coded MtGox though.
Additionally RBF result different outputs, so it can't be categorized as malleability.