You could definitely use your cyanotype pieces in a painting portfolio. It's best to think about what history, discourse, or expanded-field your work relates to the closest. Your cyanotypes exist between photo, painting, and craft histories, but your established body of work is clearly painting.
In regards to the question if lack of consistency is viewed as a weakness or strength, it really depends on the program and how you write about your work. Personally I like to see evidence of experimentation and growth mindset, rather than someone that thinks they have everything figured out.