Why? Is the business so hard up that they need to risk physical violence for $25 worth of merchandise should the police not track them down?

I understand why the shopkeeper would make this decision in the heat of the moment, but it's always a mistake to try and physically confront somebody committing a petty crime directly. They were even outnumbered!

Ultimately the confrontation actually was a huge boon to the shopkeeper, due to Oberlin's bungling of the situation, but that's not in any way repeatable. It's simply not worth the risk of being forced to commit violence and/or have violence inflicted upon your person for a few bucks.