That is a common and often misunderstood section of the Gospel.
See http://midwestapologetics.org/blog/?p=634
Christian, I’m sure that many believers would agree with you that wherever Christians are gathered, there Christ will be too, and that we don’t need a building, pews, etc. However, that is not at all what this verse is teaching. The context just does not support such an interpretation. So I would urge you not to misuse this passage just because that’s what you want it to mean. We need to let Scripture transform our thinking, rather than allow our thinking to transform Scripture.
I read it and understand about the church discipline and the God given ability of the Church to make binding decisions and act in the place of God. However the verse is a complete statement. In and out of context it says the same thing and that is that even though Christ is indeed in us from our Baptism he is also moves amongst us when we assemble in Church. Those who use it as an excuse not to go to church misread it totally. However that should not prevent someone praying with others when they feel the need and for them to believe that Christ is with them when they do.
BTW there would not have been a church at the time this was said - there would have been the Temple or local Synagogue and/or there was the disciples who followed Jesus.