Yes, but by "church", he never meant institutions. He meant the body of believers.
Some will always see an assembly as an institution. Also, the longer something remains, the more institutional qualities it takes on. Some churches handle that reality better than others.
Like many terms in the bible there is room for multiple meanings of church. Body of believers. Gathering of Christians and non-Christians that either aren't evident or who are openly inquiring into the gospel. Many are called but not chosen. Called out = ekklesia. It might even be possible to escape the pollution of the world by knowing Jesus then get entangled again (wiser souls than I can debate whether that's an 'ypothetical).