I realize that an employer cannot make contributions to a Roth IRA; only the owner (pastor) can. However, can the church deduct an amount from the pastor's pay and make the IRA payment directly to the bank or company that administers the pastor's Roth IRA account? (Realizing that the contribution has to be added to the Pastor's gross income reportable on Form W-2.)
Yes. This facilitation is permissible; essentially, it's no different than withholding from the pastor for any other "convenience" payment that is not a statutory / tax-free benefit. The same conditions apply relative to contributions to a Traditional IRA account on behalf of the pastor.