I've been collecting notes on the Knights of Malta lately, though I'm still not sure whether it all amounts to anything or is just another would-be conspiracy theory that doesn't quite add up. But there are a lot of CIA connections, ties to French intelligence and the P-2 Lodge in Italy, and links to the shadier side of US involvement in Latin America. James Jesus Angleton was a member, and apparently William Buckley (who was himself a CIA officer in the early 50's) as well.
There's a page on the Knights of Malta at
http://www.mosquitonet.com/~prewett/caqsmom25.3.html which implies that they were involved in General Edward G. Lansdale's getting Diem installed as Vietnam's president in 1955. And there's some stuff on the CIA at
http://www.umsl.edu/~skthoma/cm.htm which names Lansdale as the prototype for both The Quiet American and The Ugly American, two books mentioned in the piece cited in the original post.
There's also the fact that the Christian Anti-Communist Crusade, founded in Iowa in 1953 by Australian evangelist Fred Schwarz, was underwritten by Schick razor king Patrick J. Frawley, who was a Knight of Malta and a leading figure in right-wing Catholic circles. CACC was active in Honduras and El Salvador in the early 80's and had many connections with the World Anti-Communist League.
Although the details still aren't clear to me, it's apparent that the close political ties between evangelical Protestants and right-wing Catholics go back to the early 50's and have been tangled up from the start with fanatical anti-communism, with the CIA, and with other covert operations abroad.