So, it sounds to me like as long as the OP is not having his students run over 5 miles as part of his pitching program he is not doing anything to harm his students. Maybe not the optimal thing, but nothing harmful. So what we are really talking about is thinking that an instructor should add some sort of sprint routine to their training regimen. If he did that, the workout routine would be taking a step in the right direction to being optimal.
Although running 2-3 miles is not harmful, it WILL help in the overall physical shape of the player. I'm just not sure the OP deserved what he got for doing something that is not harmful and not the optimal thing to do. Maybe the message shouldn't be "don't distance run, period" and should be more along the lines of "short distance running of less than 3 miles is OK, but to get the optimal workout for your player, you should implement a sprint routine as well".
If I'm wrong, let me know. I'm willing to listen.