William III was still supreme governor of the Church of England during his reign. The fact that William was Calvinist did not prohibit him from being the Supreme Governor. James II was a Catholic, but due to his position as King, he was also the supreme governor of the Church during his three year reign (Miller, James II, pp. 153-154).

Further, Calvinism was not a separate church in England during the seventeenth century. There is a long historiography on this, but suffice to say that many scholars agree that between 1590-1625, there was a "Calvinist Consensus" among the clerics, bishops and theologians in the Church of England (Tyacke, Anti-Calvinists: The Rise of English Arminianism). Even the dissenting scholars admit, for the most part, that James I and Archbishop Abbot held Calvinist sympathies. James I forbade the discussion of controversial religious disputations, but this was less to punish Puritans, and more to promote harmony and unity in the Church of England (Lake, Moderate Puritans; Fincham, Prelate as Pastor; White, Predestination, Policy and Polemic).