I have been put into an awkward situation at work. I work at a 24 hour supermarket, and lately there has been a homeless person staying in the store most hours of the day. He has even started sleeping on a bench inside the store. Though, he does not sleep on it lying completely down, just at a 45 degree angle.
Management is aware of this but choose to do nothing because they say he buys things usually 4 or 5 times a day. I don't doubt that he buys things on a regular basis. But at what point does that become inconsequential when you are talking about someone who spends on average between 18 and 20 hours a day inside the store?
Shopping is one thing, but sleeping and otherwise living is completely different, right?

Loitering in MA
That must be an awkward situation. However, if the owners don't care, then that is really the end of the analysis. The owners could have the man removed. However, since the owners have instructed you to leave the guy alone, it would be unwise for you to call the police.