I just did a search on some of the Greek Fathers and their understanding of "by him", and first of all Cornelius a Lapide (not a Greek Father by the way, but great commentator) gave a great explanation about it. Here is what he said
Observe that when it is said by Him, the preposition by does not signify an instrumental cause, or a minister, as though the Word were the instrument, or minister of God, by which He created all things, as Origen supposed, and also the Arians, but it signifies an original, or chief (principalem) cause, as in Prov. viii. 15, “By me kings reign,” and 1 Cor. i. 9, “Faithful is God, by whom ye have been called” (Vulg.) The preposition by in this and other places is referred to God the Father, who is the First Cause of all things. And by here means that the Word with the Father is the original Cause of the creation of all things. So S. Chrysostom, Theophylact, and Euthymius on this passage, and SS. Athanasius, Basil, and others against the Arians. Wherefore also S. Paul (Heb. i. 10) interprets Psalm cii. 26, “Thou Lord in the beginning hast laid the foundation of the earth, and the heavens are the work of Thy hands,” of the Word, or Son. “Never, certainly, would he have said this,” says S. Chrysostom, “unless he had believed the Son to be the Founder, not a minister, and that the Father and the Son were equal in dignity.”
You will ask, Why then does S. John use the preposition διὰ (per, or through) instead of ύπὸ by, when he says that all things were made through (διὰ) Him? 1. That he might signify that the Word proceeds from the Father, and is begotten of Him. “Lest any one should suppose,” says S. Chrysostom, “that the Word was unbegotten.”
- That he might signify that the Word is the Idea of created things, according to which the Father with the Son created all things. For an artificer makes all the works of his art by an ideal, or conception, or mental word, or plan. All these similitudes are transferred to the Divine Word, who is the Begotten but Uncreated Wisdom.
As for ancient Greek commentators
By calling the saints ‘slaves’ of Christ, he safeguarded his divine nature. For to whom would human beings belong, other than to the creator and maker of humankind? And who is the maker of humankind and of all creation? Nobody except the only Word and Son of God. For “all things were made by him,” says the present writer in the Gospel. (Oecumenius 6th century Com. on Rev. 1:2)
St. Cyril of Alexandria
For if all things were made by Him, He will be Other than they all. For in this, All things, there is nothing which is not seen among all things. As the blessed Paul too is found to have understood the all things: for when in one of his Epistles he was discoursing of our Saviour and said that all things were put in subjection under His feet, excellently does he subjoin, For in that he saith all, he left nothing that is not put under Him. Therefore since we believe that all things were made by the Son, we will not think that He is one of all, but will conclude that He is external to all, and severing Him from the nature and kin of things originate, will at length confess that He is none else save God of God by Nature. (St. Cyril of Alexandria On Jn. 1:3)