Jesus drove the sellers out of the temple and emphasised not to make his Father's house a market place.
Francis was as zealous for the Lord and his will as he was for all the churches around the world.
He wanted them respected for what they are and represent; he did not want to know about turning them into what God is not.
This even though Jesus had made it clear to him that his zeal was for the Church, the assembly of believers, the living temple of Christ.
In the Sources:
"He had no blush to ask the small things of those smaller than himself; he the true lesser, who had learned from the Supreme Master the greater things.
He used to seek with singular zeal the way and manner of serving God more perfectly, as it pleased Him best' (FF 1205).
Moreover: "Truly with joyful devotion he wandered among the heavenly abodes, and in complete self-abasement, he dwelt as if hidden in the wounds of the Saviour [...].
His safe haven was prayer, not of a few minutes, or empty, or pretentious, but deeply devout, humble and prolonged as much as possible" (FF 445).
But with regard to the reparation of S. Damiano:
"It is this place where St Francis, guided by divine revelation, began the Order of Friars Minor.
Precisely by the disposition of divine Providence, which directed him in all things, the servant of Christ had materially restored three churches before founding the Order and devoting himself to preaching the Gospel [...].
For just as three buildings were repaired, so, under the guidance of this holy man, the Church was to be renewed in three ways: according to the form of life, according to the Rule and according to the doctrine of Christ which he proposed" (FF 1050).
He had taught his brothers to recite this prayer near every church they encountered, adoring the Almighty:
"We adore you, O Christ, in all your churches [...]" (FF 401).
The zeal for the house of God devoured him.
"Take these things away from here, and do not make my Father's house a marketplace" (Jn 2:16b).
Dedication of the Lateran Basilica (Jn 2:13-22)