If miners are decentralized, that means, many of them, each with a small hash rate, variable (today you are a miner, tomorrow, you aren't) and anonymous, then miners are locked into the Nash equilibrium of immutability.   In a truly decentralized system, there's no way to "come to an agreement" because the entities are supposed not to collude, not to make agreements !  The only way to have agreements in a large decentralized system, is to have a central authority proposing a SPECIFIC change, and no other, and have people come to a from of "voting": both are centralized protocols.

However, what is wrong in bitcoin is this:
"Because the miners do not form an identifiable set, they cannot have discretion over the rules determining transaction validity. " (from your link)

But miners DO form an identifiable set right now.  There are 20 of them, of which 5 are majority already.  People are cursing them, or begging them, to "do" something.