He's certainly referring to the "European Wars of Religion," rather than the concept of any war with a religious component. It's a somewhat-broad category that encompasses most of the major political struggles of western and central Europe from the 16th to 18th centuries.

Most American historians say the Wars of Religion, as a category, end with the peace of Westphalia in 1648. It's not the last war with a religious component, even in Europe, but it's (mostly) the end of a particular period where Europeans were frequently fighting, first over the very existence of Protestant churches, and later to resolve the role of a modern state relative to the church. The "Westphalian order" more or less resolved that question for western Europe. Protestant nations typically entrenched their respective national churches as minor arms of the state, while Catholic nations tended to give the church much more significant autonomy. Before the end of the 30 years war, you already saw the political relevance of the Protestant v. Catholic question evaporating as Catholic armies loyal to the French ended up assisting the Protestants, and religious lines collapsing to correspond instead to European national ambitions.

John Morrill specializes in the English Civil War, so I'm sure he can defend the idea of it being part of that struggle, though anecdotally I've more often seen them written as a struggle between Parliamentarians and Royalists, with the status of the Church of England being relevant but not the crux of the dispute.