Complex sentence: Even though congregationalists wanted each church to have its own governance, they generally opposed separation from the established Church of England, which they continued to view as being the true church, but a church that nevertheless needed reform from within.
Split into simpler sentences: Even though congregationalists wanted each church to have its own governance, they generally opposed separation from the established Church of England. The Puritans continued to view the Anglican Church as being the true church, but one needing reform from within.