After school is optimal if parents will pick up their kids. You have a longer time and they can go right home after if it's raining a little outside. Yes, you do need to be successful with presenting this to the principal and P.E. teacher. I'd be prepared to discuss a few of the programs happening around the country. Perhaps you could summarize the ones described in the Sept. RW article.
Many schools make joining the running program optional.
You'll have to work with the school system and parents on this to see how they want to handle participation. Check back at this site. Oh, don't neglect the curriculum tie-in angle. They can do journal writing in school about their running. You can map a route across the country and add up miles as they run, tracking their progress.