I have never understood running itself as a punishment. However, I am a big fan of motivation through the cardiovascular system. Sound strange that I would type this doesn't it? Well to run as a punishment will produce negative results. However, running can be done in such a way as to motivate the players and to increase their skill level. In other words, if you are going to run them, use a ball. Have the kids catch more balls in an intensive workout. Put conditions on those fielded balls to allow for reward and, yes, run to fence and back if they miss x out of x amount. Outfielders will have a lot of running to do but all infielders can be worn out as well catching balls to their left and right.
I believe any time a coach has punishment in mind after a game, they need to give it a day's rest and think about it. I believe one other thing and that is that the team will often reflect the coach. Did he run with them?