I just upgraded to El Capitan and had same issues, so I found this thread. I'm one of those who hates too much of control and pushing certain applications or workflow direction from certain manufacturers, and yes, I'm perfectly happy with PM handling my CF cards, so I really don't need Apple's Photos taking care of this (not to mention it's annoying when on deadline to handle other apps which shouldn't be there).
My solution, and yes I know it's really dirty one... Disable Apple's system integrity protection, and then you are actually allowed to delete content of Photos app. You are still not allowed to uninstall it, but at least this way it can sort of disable it, so it doesn't bug you everytime CF card is inserted into reader.