Christopher at Against the Grain has an excellent post called "Towards a Critical Appreciation of Thomas Merton " which is well worth reading for a balanced look at Thomas Merton. In the current Crisis Magazine Fr. Ray Ryland wrote an article about his time while still an Anglican priest about his interaction with Thomas Merton. At the end of the article he writes:
"Shortly after his death, Merton’s secretary Patrick Hart, stated definitively that at the moment of his death, Thomas Merton was a devout Catholic who had no intention of deserting the Faith. Indeed with the blessing of his abbot, he was going to start a new Trappist foundation and had preliminary conversations about it with people in both Washington state and Alaska."