I disagree, Steve. Non-profit organizations should not lose tax exemption because of political speech or action. Doesn't that seem to you like a direct violation of the First Amendment, "Congress shall make no law respecting an establishment of religion or prohibiting the free exercise thereof"?
If their political speech is an endorsement and is done represnting their organization, they need to lose their status.
If OTOH they make their endorsement as private person(s), then it is (and should be) protected.