In theory, ECAF could effect the immutability of the blockchain depending on what precise point they intervened.
No, this is not possible even in theory. If the immutability of a blockchain is broken, there is some serious bug in the software.
This is how it should go: Transaction is recorded on the blockchain. A dispute arises considering that particular transaction. An arbitrator looks at the case and makes a ruling (which is recorded on the blockchain). A new transaction based on that ruling is proposed to the network. BPs check that the proposed transaction comes from a real arbitrator, etc. and accept it to the blockchain.
All transaction are recorded immutably on the blockchain: original disputed transaction, arbitrator's ruling, and enforcement of the ruling by BPs. Nothing is removed from the blockchain, only new transactions are added to it. Just like a blockchain is supposed to work.
RE: Proposal for an incremental Constitution and Dapp layer governance on EOS