There are two principles at work here: One, pets (as distinguished from assistance animals) ordinarily do not belong in a church; two, parishioners should not concern themselves with how other congregants behave and should leave any necessary correction of a fellow congregant’s behavior to the pastor or his duly-appointed delegate (e.g., associate, deacon, usher).
You are correct that pets don’t belong in a parish, but you have no way of knowing the circumstances of the man you saw. Perhaps the dog
is an assistance animal and simply was not wearing his identifying jacket that day. While that may mean that places of business that ordinarily do not allow animals inside might refuse entry to a person with a service animal not wearing an identifying jacket, a Catholic church (and its congregants) should give the person the benefit of the doubt. If you have a concern about someone who repeatedly brings in an animal that never wears an identifying service jacket, then talk to the pastor and let the pastor take action as he sees fit.
As for
St. Pio of Pietrelcina, assuming your story is true (and not merely a legend), being a saint does not mean that he could not have made mistakes. By your own account, he apologized for kicking the dog, as well he should have if that is what he did. In any case, you are attributing a motive to the kick that your story does not support. Rather than anger over a dog in a church (a church is not mentioned), Padre Pio may not have wanted the dog sniffing around his feet (which reportedly had been affected by
his stigmata).