"...the secular state did not resolve the so-called "Wars of Religion" - the first state in which church and state were formally separated made its appearance a good century and a half after the Treaty of Westphalia. When the so-called "Wars of Religion" came to an end, the absolutist state was the victor. The way had been paved for the deification of Louis XIV.If we look to the origins of these wars themselves, further problems...arise. Can they really be called "Wars of Religion" if Catholics killed Catholics, Lutherans killed Lutherans, and Protestants and Catholics often collaborated? Holy Roman Emperor Charles V spent most of the decade following Martin Luther's excommunication at war, not against Lutherans, but against the Pope. When the Lutheran princes did take up arms against the Catholic Emperor in the 1550s, they did so with the aid of Catholic France.The French "Wars of Religion" are full of collaborations between Protestants and Catholics, and the Thirty Years' War - perhaps the most notorious of the "Wars of Religion" - saw Cardinal Richelieu throwing the full force of French might on the side of the Lutheran Swedes, who in turn attacked Lutheran Denmark. While the Calvinist Dutch were helping the French royal forces to defeat the Calvinists at La Rochelle, Catholic Spain was supporting the Protestant duke of Rohan in his battle against the French crown in Languedoc. The Thirty Years' War was, in fact, primarily a contest between the Habsburgs and the Bourbons, the two great Catholic dynasties of Europe."This is an interesting development not only in itself, but also for its apologetic value.
The above quote is taken from a debate between Cavanaugh and fellow academic Russell Blackford on the Religion and Ethics website of the Australian Broadcasting Commission. See also Cavanaugh's earlier piece, 'The Wars of Religion and Other Fairy Tales' on the same website.