You said, "While I agree that the problems you mention here do exist in the modern church, I would like to point out that God still has many faithful churches and church leaders who do not 'hold the people underwater.'"

That wasn't the scope of the vision. Part of the scope of the vision was that generally speaking, pastors keep the body of Christ in bondage, knowingly or not. And for those who realize that there are different types of 'bondage' and that 'bondage' manifests in different ways, it's true. 

Furthermore, God often speaks in generalities in order to communicate important or/and 'majority truth' as well as to cut to the chase (and allow the Holy Spirit to explain further for those who need it). Jesus included all the Pharisees when He rebuked them. Yet, He knew about Pharisees like Nicodemus (and Joseph of Arimathea) and other Pharisees who welcomed Him into their hearts and homes, but Jesus never specifically distinguished the godly Pharisees from the ungodly ones. This was because there's a time to generalize and a time to be specific, and when Jesus was talking to crowds of commonfolk or groups of Pharisees, generalizing was proper. When He talked to Pharisees individually, then being specific would be fitting. The apostles also accused Jews who weren't present at Jesus's death for His death because in that context, though Stephen later lost his life because of the same principle, it was proper to state that all Jews (just like all men) killed Jesus. 

I think when God makes a generalization we should just let Him do so. If we need an explanation we should ask Him for clarification rather than saying, "Not so, Lord."