In Ephesians, Paul talks a lot about unity in the body of Christ, the church.
Saying that the body of Christ is the church is not the same thing as saying that the church is the body of Christ. It is our connection to Christ that makes us part of the body of Christ. Being a part of the church, or a church, does not connect us to Christ.
The same thing applies to the unity Paul is calling us to. Having unity in a church or denomination I belong to is not the same thing as having unity in the body of Christ, the church. And in many cases, the things that might unify a church or denomination end up causing division in the body of Christ.
We are united by Jesus death on the cross. We now share the same Spirit and have equal access to the Father!