The Queen’s Agent: Francis Walsingham at the Court of Elizabeth I by John Cooper Faber & Faber, 2011, 400 pages, $24.99   The History of England: Vol. II: Tudors by Peter Ackroyd Macmillan, 2012, 503 pages, $32.99   Even now, Oxford University’s Tudor era historian John Cooper gives the impression of clearing his throat and lowering his voice in awkwardness as he begins a chapter on the Catholic English mission nearly 450 years ago. “The story which is about to unfold,” he writes, “is deeply contested … The myth that Catholicism is somehow alien to Englishness has had a long…