A few points

First of all, obstruction occurs when contact is made. Therefore, players slowing down will never lead to it being called. At older levels I teach to run through and if contact is made obstruction will be called. At the level you are speaking of I would talk to the other coach and the umpire (when there is one). One additional note, for that level maybe you should try the safe bases, where there is one base for the first baseman, and one for the runner.