No, your friend is not right when he claims that the Dead Sea Scrolls (and for that matter other writings from the ancient world) disprove the Bible.
In fact, the opposite is the case. Far from disproving the Bible, these ancient manuscripts repeatedly confirm the accuracy of the Bible and have helped us gain new insights into the world of those who lived during Bible times.
As you may know, the Dead Sea Scrolls were discovered almost 60 years ago in a series of caves near the Dead Sea. Scholars agree that these ancient manuscripts—written shortly before the life of Jesus—are one of the most significant archaeological finds in modern history. Many contain books of the Old Testament, and have repeatedly confirmed the accuracy of the texts of our Bibles. Other scrolls show that many people were eagerly looking for the coming of the Messiah.
From what you say, I suspect your friend's real problem is that he doesn't want to face his need of God. Even if all his questions were answered (as they could be), he probably would still refuse to believe in Christ because he wants to run his own life. He is like the people of whom Jesus spoke in one of His parables, who shouted, "We don't want this man to be our king" (Luke 19:14). Pray for your friend, and ask God to use you to help him see his need of Christ.