An interview with Jeffrey Sposato, a Mendelssohn scholar and author of "“The Price of Assimilation: Felix Mendelssohn and the Nineteenth-Century Anti-Semitic Tradition," features some very interesting remarks about Mendelssohn's religion and the effect it had on his career and legacy.
Read the interview here: http://www.brandeis.edu/now/2009/june/sposatomendelssohn.html
"Despite the fact that Mendelssohn, who was born Jewish, had been baptized as a Lutheran at age 7, most post-war scholars had described him as being very attached to his Jewish heritage, and that his views never changed over the course of his life. As a child of Jewish and Catholic parents myself, who has changed his views on religion many times over the years, I found such a monolithic description of Mendelssohn hard to swallow, especially given the tremendous amount of Christian sacred music he composed. What I found in my research. . . is that Mendelssohn’s views towards his heritage changed radically over the course of his life. At first, while under his father’s watchful eye, he attempted to distance himself from Judaism, often by incorporating anti-Semitic imagery into his oratorio texts, but later, when his father was no longer in the picture, Mendelssohn worked to find ways in which he could celebrate his Christian faith in his works without denigrating the Jews in the process."
". . . despite Mendelssohn’s status as a Christian and that generations of his progeny were all Christians from birth, the Nazis viewed them as ‘tainted’ by Judaism even in the 1930s."