This is not WRONG. Churches should not be involved in endorsing candidates. They are tax free because they are not a political organization. If they want to pay taxes, their FREE SPEECH can be exorcised. Every "Religious" non-profit entity knows the rules when they get their IRS status.
However, there is pressure to construe the restrictions more broadly than endorsing a candidate, and to speak out on issues generally, like same sex marriage if there is a referendum. I would hope the tax restrictions would be construed narrowly so as not to eviscerate the rights of churches to speak out substantively on moral issues of the day without fear of losing tax exemption.