He's putting the bureaucrats at the IRS in a quandary: they can't say "don't pray"; thus , within the confines of any policy cooked up at the IRS, the churches would be able to slightly modify the previously suspect "voter guides" etc, and be quite immune from ACLU harassment.
Let the IRS clarify!
I understand your point, and it's well taken.
I just don't see the need in validating the IRS's involvement in matters of faith, or anything else.