This is the command by Jesus to St. Francis.
I think we must remember the setting of those times. When Francis speaks of Christianity in his famous paper “Mirror of Perfection” he is only speaking of the Catholic and Orthodox Church. There were no other christian religions at that time. The Institution we call the Catholic Church was pretty much dominant in Europe, even to the point of influencing and infiltrating civil structures in some cases. So it was not a weak Church by any stretch.
So we can see Jesus could not have been speaking of integrating ecumenical principles into the teachings at that time. There were Muslims,Buddhists,Jewish and various other established religions already present. The evangelical ways of bringing those into the Catholic Faith are already tested and working well for 11 centuries. It is already known that by Christ’s redemption these people are heirs to the Kingdom of God. But all the same Christ insisted that they be taught and indoctrinated into his new religion. We know that Francis in his sermons used these working methods to try to win over the souls, not only to repair the bodies or these people he was in contact with.
So Francis was working under this framework. He treated everyone with charity regardless of faith or lack thereof.
The question then is that. Other than the corruption in the Church that also was rampant, I can’t see what else there could be to rebuild/repair.