Reading 'Shogun' makes me mad at many people in history who have called themselves Christians. In this story it's the dominating Catholics and Jesuits who anger me, but there have been many Protestants as well. Sometimes these people were doing their best, but even in those cases they were often using methods that weren't Christ's. They betrayed the Lord and sorely damaged Christian witness.
Richard Bauckham says in 'The Theology of Revelation' that it's okay for Christians to use power when we can do so without compromising our principles. But if we must chose between power and integrity, we should always choose integrity. The ends never justify the means in Christian faith. We are to look to God to handle the results. Sure, this often results in martyrdom, like Jesus and Paul and many others in the first 3 centuries after Jesus. But the faith was vital then. It became compromised when Constantine made it the official religion of the Empire.
All of this said, centuries of disgraceful behavior does not disqualify the testimony of many Christians who have lived lives of integrity, the Scriptures, and Jesus.