Did St. Francis of Assisi become an angel after his death?

No. The Church teaches that angels and human beings are entirely different orders of creatures and do not transform from one to the other. Since St. Bonaventure is a Doctor of the Church, I doubt he taught that St. Francis of Assisi became an angel at death. Without having seen the material you read, my guess is that your sources misunderstood St. Bonaventure’s intent. In the past, it was common for consecrated religious to call their founders “our seraphic father” or “our seraphic mother.” This was not intended to mean that the person had actually become a seraph, anymore than a mother describing her child as a “little angel” intends to say that her child actually is an angel. In the same way, it is possible that whatever St. Bonaventure actually said about his order’s founder was hyperbole that has been misunderstood.