The goal with middle school kids is to teach them to run the entire race without walking. I would tell them during practice that I don't care how slow you have to run but I want you to run the entire time. I would start of with only having them run 15-20 minutes and after about a month increase to about 25-30 minutes for each run. I would not do any interval training with them! Who cares if they run fast in middle school. Let them learn about easy aerobic running because in the long run it will make them faster. Also, I suggest doing form drills before the runs a couple days a week and after the runs have a fun game that keeps them running around. Examples are ultimate frisbee, elbow tag, etc....
Example Practice
1. Form Drills (high knees, butt kicks, skipping, fast feet) Here is a link
http://www.runningplanet.com/training/running-drills.html
2. 15-30 minutes of easy running. Encouraging them to not race the run but to not stop and walk either. Also, avoid busy roads with the youngins.
3. A fun game that involves running!