You need to sit down in a room with the CEO and CTO, and have the CTO describe his concerns and then you can all resolve the issue together. For the sake of the culture of the company you can not let this slide as back-room talk, as that would create a poisonous culture. When that is answered talk to a lawyer before signing any papers, and remember that the companys lawyers are obligated to protect the company and not your interests so really get your own laywer.
I don't know exact your situation but I saw similar case. In summary, the founder who showed support to company without ego made company successful, not the CTO or VP engineering who joined later stage. That’s your baby, but to CTO, that’s neighbor’s. You are happily clean up your baby’s diaper or mess, while neighbor will blame you and not clean up. If you need process to get enterprise ready, you can hire process guy and experienced enterprise software guy and adjust your team. I think when CTO say it to you, he have talked CEO already. In that case, if CEO is mature, CEO should stop CTO blame you and discuss that matter with you first. If you are not sure about CEO’s intention, you should talk him and understand about it. In this case, I feel that CTO have hired couple of his guys and they are all point same direction. But don’t be afraid those and think whether you still can help company or not. (I think you still can help company) you should talk to CEO and let him know that company need you for technical evangelist or customer meetings or … and at last as back up to CTO. (For me, It seams CTO is a type of guy who build castle inside house, which will cause problem soon within organization.) By the way, you should consult with the lawyer if possible, and understand what you can get worst case.
