Complex sentence: Differences in approaches to religion eventually came to the fore, with the rise in power and influence of the independent faction in the English Parliament as a result of the independents' dominance of the New Model Army alarmed the still Presbyterian-dominated Scottish Parliament.
Split into simpler sentences: Differences in approaches to religion eventually came to the fore with the rise in power and influence of Independents in the English Parliament. In particular, their dominance of the New Model Army alarmed the still Presbyterian-dominated Scottish Parliament.