It seems that CKeditor automatically initializes on any element that has contenteditable=true. It even says so on their Guides page, but with no instructions on whether this can be avoided.
This makes me lose a lot of control over the content on my page. I have some content that should be editable with the rich text editor, and some other that shouldn't. But this makes CKeditor initialize on elements that don't even expect rich text, and they don't get saved as rich text in the database... So I need to get rid of it from the interface, but I don't know how...
Can I tell it to avoid automatic initialization?
The answer to the question is No.
The alternate solution, is to omit the contenteditable=true, then after initializing the CKEDITOR, set the contenteditable attribute on the required element from Javascript.