It is certainly permissible to clean up the graves and to remove most of the stones if they are causing a bother. However, I suggest that not all of them be removed since that could cause the family of the deceased a certain amount of anguish. I also suggest that it might be a nice idea to let the families know that you are planning on cleaning the graves and that you want to remove many of the stones. That way if anyone is unhappy with the idea they can contact you to let you know.