John Chrysostom

He has well said, "perhaps," that the master may yield. For since the flight arose from perverseness, and a corrupt mind, and not from such intention, he has said, "perhaps." And he has not said, therefore he fled, but, therefore he was "separated," by a more fair sounding expression softening him the more. And he has not said, He separated himself, but, "he was separated." For it was not his own arrangement that he should depart either for this purpose or for that. …

Homily on Philemon 2 ↗

Theophylact of Ohrid

Since Onesimus ran away with evil intent, Paul turns this flight into something beneficial. Perhaps, he says, he ran away by the providence of God. He also commendably calls the flight a separation, so as not to irritate the master with the word "flight." And by shortening the time, he calms his anger. "For an hour," he says, "he was separated." At the same time he also shows that however long he was with Paul, he was also with Philemon. …

Commentary on Philemon ↗

Theodoret of Cyrus

Onesimus's flight has become the source of good things to him.

Interpretation of the Letter to Philemon

Jerome

Perhaps for this reason he departed from you for a time, so that you might receive him forever. No longer as a servant, but more than a servant, a beloved brother, especially to me: but how much more to you both in the flesh, and in the Lord." Sometimes, evil is the cause of good things, and God can turn the wicked intentions of men to good. What I am saying will become clearer through an example. Joseph's brothers, incited by jealousy, sold him to the Ishmaelites for twenty pieces of silver (Gen. 37). …

Commentary on Philemon ↗

Thomas Aquinas

Then when he says, Perhaps, indeed..., he gives the reason why he ought to receive him kindly, first, on the side of God, second, on the side of the Apostle: If therefore you count me as a partner...; third, on the part of Philemon himself: Trusting in your compliance... On the side of God, because the providence of God often permits what is evil to come about, in order that good might follow from it, as is clear from the sale of Joseph, that he might free Egypt and the family of his father. …

Commentary on Philemon ↗