If the church building isn't the new temple, then should we put this whole Temple comparison on the shelf?
I'm tempted to do just that. The passage still has meaning and application, even without this type of connection. In fact, this type of equivalence usually drive me crazy and leads to poor application.
But, in this case, it's called for.
In John 2, Jesus goes from talking about the Temple to talking about his body. He used an awkward pun to make that transition, working off the word "egereis," which means "to raise." To clarify the awkward pun, John inserts a comment that the Temple Jesus was talking about was actually his body.
Throughout the New Testament, the image of Christ's body is connected to the Church. Membership in the Church...speaking about belonging in the Church as "membership" actually has it's origin in language about the body. A body is made up of many parts, or "members." Before anyone talked about "member of a club or organization," they talked about "members of a body."
Normally, we wouldn't do this math.
Temple = Body
Body = Church
Temple = Church QED.
It's just as easy to show:
God = Love
Love = Blind
Ray Charles = Blind
Ray Charles = Dead
God = Dead QED.
So, why would we say that the Church is the new Temple?