In a word, yes. It’s unfortunate, and I don’t think they should be able to, but legally, they can:
The IRS has published Revenue Ruling 2007-41, which outlines how churches, and all 501c3 organizations, can stay within the law regarding the ban on political activity. Also, the ban by Congress is on political campaign activity regarding a candidate; churches and other 501c3 organizations can engage in a limited amount of lobbying including ballot measures and advocate for or against issues that are in the political arena. The IRS also has provided guidance regarding the difference between advocating for a candidate and advocating for legislation. See political and lobbying activities.
So although I’d like to see churches lose their carte blanche 501c3 statuses unless they are actually able to prove they deserve it, while they have it, they can still support (or not support) Amendment One and other such issues. They just can’t support specific candidates.