Saying that the early Church chose the books that constituted the Bible is like telling the Native Americans that Columbus discovered America. God set the canon, the Church received them.
Luther was in agreement with many of the early Church fathers, including Jerome, who compiled what was to become the official Bible for almost 1,000 years.
Jerome included the "deuterocanonical" books in a separate section of the Latin Vulgate because he and the other best minds of the day considered them worthy of study, but not to be considered Scripture because of the significant errors in them of time, geography, and theology. In fact, the "deuterocanonical" books were not officially designated canon until Trent -- mostly in response to Luther's rejection of them.
One might properly say that Luther didn't take away the "deuterocanonical" books from the Protestants, but rather gave them to the Catholics!
I am sorry, your analogy is wrong. Protestants (reconstructing early church from printed paper) are rather like the Columbus followers while Roman Catholics and Orthodox are like Native Americans. Bishops - the sucessors of Apostles had the power given them by God and they had the guidance of the Holy Spirit in writting and selecting holy books. God acted THROUGH the Church and God established the Church before the books. Christ did not write any books, he appeared in person and He spoke to the living persons and He established His Church - His Body "the pillar and ground of the truth"(1Tm:3:15) made from men and not out of printed paper.
Luther was in agreement with many of the early Church fathers,
Luther was in agreement with Talmudic scholars since he trusted rabinic tradition more than he trusted Christians. That is why he removed the books which rabbis removed in the 2nd century and that is why Protestants follow late Masoretic Hebrew version of OT from IX c. (which contradicts the text of New Testament).