Among Christians there are so many doctrinal disputes. Many died making wars because of these different opinions. Why did God not intervene to clear up our understanding in order to avoid wars and disputes? Just after the Protestant Reformation eight million Christians slaughtered each other because God did not communicate the correct doctrine doctrine clearly to them.
God give us free will. We can do what is right or we can choose to do wrong. We can choose to accept the truth in the Bible or we can misinterpret it and teach false doctrine. God does not prevent us from sinning and he does not prevent us from believing in false doctrine. To expect him to force people to believe the truth is to ask him to no longer give us freedom of choice. It is to steal our freedom, which is something God will not do because he loves us. Love gives a choice, so God give us freedom.
By the way, God did intervene to clear up misunderstandings. His intervention is creating the inspired Bible. He has already given us the truth. We do not need more truth. What we need is to accept it and to apply it in our lives. The fact that there are false interpretations does not point to a problem with God but with us human beings.
I assume that you are referring to the thirty years war, which happened more like one hundred years after the Reformation, starting in 1618. The numbers you have heard are probably a bit exaggerated. Estimates are more like five million deaths, but I suppose the exact numbers do not matter to your question. This was a terrible war, as are all wars. Just so you know, this war did NOT happen because of disagreement over doctrine. It happened because of greed, desire for power, selfishness and all the other reasons that almost any war happens. There was a slight religious component to the cause of the initial phases of this terrible event, but once it got started, the religious component virtually disappeared. In this terrible war Protestant fought against Protestant and Catholic fought against Catholic. The fight was principally over which of the great European dynasties would achieve the greatest power and wealth. Even the religious component was not over a doctrinal issue but over the question of who chose which religion was to dominate in particular states. It was over religious freedom rather than doctrine.
In any case there is one really clear doctrine that God has communicated to us, which is that we should not be killing our enemies. Most definitely we should not kill those who disagree with us on a religious matter. To say that Christianity caused these wars is to commit a rather large error, to say the least. In any case, there was nothing for God to clear up on this matter. All sides in this terrible war were well aware that killing other Christians in the name of Jesus is totally unacceptable. Again, the cause of this war was greed, desire for power, pride and selfishness, it was not over the doctrinal differences between Protestant and Catholic.