I coach middle school, but we use the same facilities as the high schoolers and I'm always on top of what they're doing. One day the summer before last a freshman came out. He was a skinny little runt and about as awkward and uncoordinated as they come. Since I didn't have any middle schoolers that day I decided to run with him on his first day of practice. He didn't make it 400m at 10:00 pace before having to talk. We repeated that several times and he never got much more than about 600m before needing to walk. He missed the next two days but came back out later in the week. I thought he had quit.
During XC that fall he never broke 25 minutes for 5k. He kept training though. During track he ran 6:40/14:30 for 1600m/3200m respectively and didn't break 3:00 for the 800m. He got last in a couple of meets. But he kept running.
This summer he kept building on what he did and worked his way to where he could do the easy days with the top guys/girls (16:30 boy/18:00 girl). Sure they run their easy days way too slow, but it was good for his confidence. As a 10th grader he nearly broke 21 minutes for 5k and never ran over 22 minutes. I'm quite excited to see how he does during outdoor and I bet he'll be real close to breaking 20:00 as an 11th grader.
I've had other kids improve a lot (from 9:00 for one mile to 14 minutes for 2 miles in one year), but he's the most drastic I've been around. He'll never break 16, but he works hard and I'm more excited to watch his improvement than anyone else.
So 13 minutes isn't bad for a freshman. Who cares if they never make varsity? Running is about doing one's best. Outside competition is secondary to competing against one's self. You need to stress that and not act like a runner is worthless if they aren't in the top 7.
As far as training I would focus on some shorter stuff. Not a ton, but slogging slow miles isn't good for anyone. The HS coach put a girl in nothing but the 3200m last year and she never broke 18 minutes. Well, on paper she did once, but that's because they figured no one could be so slow and said she was finished after 7 laps so she got credit for a 16 minute 3200m. Don't do that to anyone. 13 minutes ain't bad though.