Your argument applies to theft of any low value item. If a shopkeeper presses charges against a shoplifter, are they using public services for private gain? Should there be checks in place to stop shopkeepers from reporting too many thieves?
In your hypothetical example, I believe you are referring to a physical storefront where the primary revenue generating activity is to sell merchandise.
If your hypothetical shopkeeper had a shop that made more money from forcing shoplifters to pay a fine for scaling, then... perhaps. I don't think your hypothetical shop exists, so it's tough for me to answer.