I am friends with a Franciscan monk and trying to find out more about what he's told me. What I've gathered is that Francis could have easily splintered off from the church and been a heretic or started his own church, and that the Catholic church had to actively court him and try to keep him on a leash and prevent a schism of sorts. I've gathered he was too passive to present a real challenge to the church, but did the church see him as one? Did they change at all due to his popularity? What was the religious climate like at the time for challengers to the pope? Could Francis have become an anti-pope?
The answer to this is question is kind of two-folded. In short, I think the catholic church would have appreciated not to deal with this "challenge" that Francis and other mendicants proved to be towards the church and their authority over the scriptures. But they also needed the new mendicant orders (the Franciscans and the Dominicans) as their allies against what the church considered to be the real challange against the Churchs authority, namely the heresies of the cathars. That's why I used the quotation marks ("") when speaking of St. Francis as a challenge to the church in the 13th century. We need some background to understand why he were considered an ally of the church and not a heretic. Because it could've easily been otherwise.
In the middle of the 12th century, the Church was starting to really constitute it's power in Europe and it tried to get more involved in all parts of society. They had monopoly on writing and, to a certain degree, reading. Therefore, they were the only ones who could understand and interpret the scriptures. Around this time they started a policy of excommunicating and denouncing thoughts and interpretations of the Holy Word that deviated from the Popes and the Canons. This meant the Cathars and the Waldensians, among others. The Cathars have since become famous for being the target of the crusade towards Albi in Southern France (1209 - 1229), which is the first crusade in Europe directed towards heretics. Although, they are not so interesting for this subject.
The interesting thing is the excommunication of the Waldesians, which in many respects thought a similar doctrine to that of St. Francis. Phillip C. Adamo and Joseph H. Lynch have said that what separated them most in the eyes of the Church was St. Francis' loyalty to the Church. But there was also another thing that separated them, namely the situation. The church had tried to excommunicate and pursue the mendicants of the 12th century. But they persisted, and some even continued to gain popularity among the people into the 13th century. So, in a way, when Honorius III approved the Franciscans (1223) and the Dominicans (1216) as something new and different, it was mostly a new approach to deal with both the heretic cathars and to keep the mendicant preachings in line with the Canons. The Franciscan Order, I must add, did change after it gained the papal approval. The pope became somewhat involved in establishing guidelines for franciscan teaching, and this is about the same time where Francis steps down and withdraws from the leadership of the Order.
I hope this answered some of your questions. I tried to find a read thread and give a pedagogic answer. If I failed, I will answer points where I might have been vague.
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