Philip F. Gura has a useful article, "Beyond Transcendentalism: The Radical Individualism of William B. Greene," in a collection called Transient and Permanent: The Transcendentalist Movement and Its Contexts (Mass. Historical Soc., 1999), edited by Charles Capper and Conrad Edick Wright. He concentrates on Greene's philosophical and theological writings from the 1840s, but also speculates a bit on Greene's reasons for leaving the pulpit in West Brookfield in 1850. Greene's relationship to Orestes Brownson, who was an important early mentor, is also explored a bit.
Dean Grozdin's American Heretic: Theodore Parker and Transcendentalism (Chapel Hill: UNC Press, 2002) adds a bit of soap opera spice to Greene's story. Apparently, Theodore Parker was somewhat smitten with Anna Blake Shaw, who would become Mrs. William B. Greene. Grazdin gives an interesting account of the resulting conflict, drawing on the letters of Parker, Greene, Brownson and Elizabeth Peabody.
And I haven't seen it yet, but it seems American Renaissance Literary Report 10 (1996) includes Kenneth Walter Cameron's "Emerson and William Batchelder Greene's Creativity and Questing," which "reprints a number of Greene's works and articles about him."Sound like it might be good stuff.