If God ordained the reformation and the subsequent splits of Christendom which, within Protestantism alone, accounts for most of the fragments, I have to question God's wisdom in destroying the unity of the Church.
Before the reformation, there were different movements, heretics, schisms and disputes about theology. T Hey never amounted to a complete dismantling of the very structure of the Church to the point where what Church one belongs to as a Protestant doesn't really matter (since the Holy spirit can be potentially in any of those Churches). At most there were three major traditions before the reformation, all of which I would consider part of Christendom, the Catholics, the Eastern Orthodox and the Oriental Orthodox. When Protestantism destroyed the idea of Church communion at that societal and spiritual level, there became numerous state Churches, dissident protestant movements and constantly evolving forms of Christianity almost every century.
If God ordained this as a good thing he willed for the sake of the Church, instead of simply allowing it to happen due to human error/freedom, I don't know what he hoped to accomplish. I don't think the Gospel was ever lost that it needed restoring, I don't believe the Church was ever corrupted to the point that it needed a new founding and complete dismantling of the old system.