The church is identified with Jesus Christ because it teaches, and is the fountain of, his gospel. Even though the twelve had learned that there was a Father in Heaven who was separate from Jesus (who had identified himself as Jehovah, the one who gave the law to Moses, see 3 Nephi 15:5), it was still Jesus who was the head of the church. They will pray to the Father, but that prayer will only be effective if done in Jesus’s name.
Therefore, the church is built on the gospel, and the gospel requires that humankind live the commandments. If they are not living the commandments and teachings of the gospel, they will be as the stubble that Jesus had previously declared would be burned at the end. They would not enter the Kingdom of Heaven.