Was Jesus referring to the Church as we know it when He said 'I will build my church'?
No. The term translated "church" is Ecclesia, and Scripture uses it more broadly than the present-day Body of Christ. It can describe Israel as a called-out assembly in the wilderness or even a riotous mob in Ephesus, so Jesus’ statement need not refer to the Church as we know it.
Les teaches that the Gospel accounts—Matthew, Mark, Luke, and even John—are still predominantly directed to the nation of Israel, because the Church as we know it, the Body of Christ, was kept secret in the mind of God and is part of the mysteries. If it was a secret, no part could slip out. Les asks listeners to search the Gospels and see if Jesus ever hints at turning to the Gentiles and calling out a Gentile body for Himself; he says you won’t find it. The closest statement is, "I will build my church, and the gates of hell shall not prevail against it." But Les does not think Jesus was specifically referring to the Church as we know it, because the word Ecclesia, from which "church" is translated, is used in different manners and ways than just the Church, the Body of Christ. Stephen called Israel in the wilderness around Sinai the Church in the Wilderness—a called-out assembly, not the Body of Christ. In Acts, a riotous mob in Ephesus was also called an Ecclesia, translated "assembly." Paul almost always qualifies the present-day Church as the Body of Christ, or the Church which is His body.