It's easy to see why Christians would view those passages as promoting pantheism rather than Christianity.
But I am unsure whether that description of God would be in contradiction to accepted gospels. In any event, the church interpreted it's meaning as saying that anywhere one sought Christ, one could find him. Doesn't the bible say something along the line of Christ being present anytime people gather in His name? I do not know of anything written which states one must have priests or the Mother Mary as our intercessor. According to Christ, you shall only come to the Father thru him, however, according to the Church, you can only come to the Father thru the Church.