That's not how disease works. If her rats are healthy it's irrelevant. People have a very misconstrued idea of rats as being disease ridden animals - they aren't. Especially domestic rats. Chances are good her chicks poop has WAY more dangerous bacteria and parasites and protozoa in it than rat bedding would, and if you use deep litter that just sits there too, until - like the rat poop would - it gets stirred in.
OP - Do some real research into how composting animal poop works and go from there. Please don't fall for fear mongering. But DO deal with your feral rat problem - feral rats are a draw for predators and they themselves will gladly chew up chickens if they're desperate.