I don’t the argument is how much tolerance we should have over shoplifting. I think the argument is how much tolerance do we have for the murders, rapes, assaults, home invasions, etc that WILL occur if the bad guys are emboldened to commit organized large scale thefts with absolutely no fear of consequences.
So yes, store owners should be encouraged to protect property with force. Lots of it.
You're on the right track with your thoughts. If this keeps up the natural progression is that a dominant movement, gang or warlord will arise to bring it all under one umbrella, then there's real trouble that will be hard to confront. As the normal channels of the economy fall the blackmarkets will rise as a supplement if not a replacement for consumer needs and criminal organizations will be in the forefront at providing those needs.