The reaction path Smoluchowski equation approach developed in a recent work to calculate the rate constant for a diffusive multidimensional barrier crossing process is extended to incorporate the configuration-dependent diffusion matrix. The resulting formalism is then applied to the investigation of stilbene photoisomerization dynamics. Adapting a model two-dimensional potential and a model diffusion matrix proposed by Agmon and Kosloff [J. Phys. Chem.,91 (1987) 1988], we derive an eigenvalue equlation for the relaxation rate constant of the stilbene photoisomerization. This eigenvalue equation is solved numerically by using the finite element method. The advantages and limitations of the present method are discussed.