Surprised it's taken Ryanair so long to be honest.
I should think they just need to make an announcement before boarding or put a card on the affected seats that say "€15 extra for each of these exit seats". The people that paid it will have some extra note on their e-ticket or maybe they get given a nice coloured piece of card at the desk or something. If you sit in the marked "€15 extra" seats having not paid the supplement so don't have the note on your e-ticket or whatever, and then someone boards late that did pay it, then you get turfed out of the seat and left to choose a seat from whatever odd seats are left throughout the plane. It's only around 12 seats that are affected, so anyone that didn't pay the charge and then is foolish enough to not immediately comply when asked to vacate the seat for a passenger that did, should be easy enough to handle.