Kotoamatsukami would let Danzo win this easily... He wouldn't need Izanagi and I doubt he'd waste it, since he's saving it for his fight with Tobi. There was a reason Danzo wasn't made to interfere in the story.
I honestly believe that even without Naruto, Danzo and Root could've defeated Pain. Imagine if Kishimoto hadn't handicapped the Leaf Village. Team Guy was out on a mission, as were Anko, Yamato and Sai. Danzo hid because of his ulterior motives, he wanted Tsunade to be killed and Root to act as the saviour. Remember how big Root was?
You must be registered for see images
It was an entire counsel-worth of the Leaf's worthy ninja. They were all strong, heartless shinobi. With these guys added to the fight and Guy & Kakashi teaming up, Tsunade protecting the whole village and Shikamaru working out the trick behind it, Danzo and Root could defeat Pain mid difficulty in my opinion. Danzo alone though? Eh.