IANAL, but if the operating agreement is set up so that the CEO has a specific power, then the next layer up would be for the shareholders to amend the operating agreement. If the CEO and CTO are equal partners, neither would be able to obtain a majority vote and the operating agreement would stay as it is - assuming, of course, that the agreement requires a majority vote for amendment.

It sounds like the CEO de facto controls the company in this case, and can ignore the other shareholder at will. He could block communications with him and basically have a silent partner.