Does the Supreme Court's decision in Kennedy v. Dupont Savings & Investment Plan apply to church pension benefit plans as well as ERISA plans?

Probably not unless a IRC section 410(d) election has been made or the church plan does not meet the definition of 'church plan' set forth in ERISA section 3(33). See ERISA section 4(b)(2) for the application of Title I of ERISA to church plans, which Title is what the Supreme Court was interpreting and applying in Kennedy.