Malleability is already fixed. Segwit does not fix it further.
Technical point: This is very much not the case: Malleability is blocked in the relay network for a narrow class of transactions but anything clever is exposed, multisig is exposed to other-signer malleation, and all transactions are exposed to malleation by miners. Segwit fixes it in a deep and profound way for all purely segwit transactions.
doesn't say anything about a 1MB block size in the Bitcoin whitepaper. Changing it to 2 MB (like we did) does not change the protocol
The whitepaper doesn't say anything about 21 million coins-- or a great many other very important consensus rules. If the rule was intended to _simply_ be temporary it could have had an automatic phase out, but it didn't. If it was intended to go up as it filled, it could have-- just as difficulty adjusts, the mechanism is all there.
Already Ethereum users make the incorrect argument that bitcoin was hardforked in the past to fix the value overflow bug (it wasn't) and thus its okay for them to manually tamper with the ledger to claw the funds the DAO lost and hand them over to other users. You're seeing a first hand demonstration for how quickly people cling to argument of convenience.
The rule by math element of Bitcoin is essential to the value proposition, great care should be taken to not erode it based on short term interests.