I'm pretty sure the chickens will be fine. They might peck at it because it will stick out but you can just cover it up with something. Another thing is you can keep the chicks in something smaller, and indoors with a heating lamp until they're older.
Have you considered white washing it? I plan on whitewashing my coop here once we've sheeted the inside. It's a white paint, but has hydrated lime in it which kills mites/lice. Not only does it look 'fresh', but it's easier to clean (you can't wash something off plywood) and kills the bugs! A friend of mine whitewashed her coop...looks Great!