Complex sentence: The party of divines who favored presbyterianism, or government by hierarchies of elected assemblies, was in the majority, but political and military realities led to greater influence for the congregational party, which favored autonomy for individual congregations.
Split into simpler sentences: The party of divines who favored presbyterianism, or government by hierarchies of elected assemblies, was in the majority. However, political and military realities led to greater influence for the congregational party, which favored autonomy for individual congregations.