Thanks everyone! I'm still going back and forth in my head. I am concerned it will be viewed as being unable to follow instructions, although as the CEO of the organisation knows me / has worked with me before (not as my manager, as a partner to the organisation I currently work for), I imagine I may get a little more benefit of the doubt than someone going in completely blind. Similarly, the organisation has also worked with the referee in question, so it would be very easy for them to verify it.
I could include her as a referee on the CV, but it would be difficult for a potential employer to contact her as she lives overseas. Therefore her reference would be a written one anyway.