Nicholas inherited a situation not of his own doing. Solzhenitsyn, in the Templeton address (linked above), points to schism in the Church and Peter the Great as the causes of Russian turn to secularism.
True, but what he did about it was generally not optimal, either.
I'm far from an expert on the subject, but it's quite reasonable to see Peter the Great's "modernization," particularly his importation of Western European intellectuals, as a secularizing force.