I don't know about whether they were joking or serious, but I think their point was that for any person, there are probably some charities they'd object to funding. I know people who won't donate to Habitat for Humanity (US charity that builds houses for poor people) because of their religious proselytizing. There are Catholic charities; there are charities that distribute birth control; there are even white supremacist charities. Aside from religious considerations, while charities in the US generally can't directly engage in political activity, there are lots of charities that are connected to political organizations, all across the political spectrum. Pick any controversy (climate change, gun control, religious freedom, reproductive rights, etc.) and I bet you could find charities aligned with either side of the question.

I'm quite serious.

http://www.salon.com/2014/08/21/cincinnati_archdiocese_to_ca...

The article quotes a vatican directive about stem cell that uses the phrase "cooperation in evil".

http://www.bostonglobe.com/metro/2014/06/28/protesters-gathe...

The article mentions a 1994 incident in which a gunman murdered two people and injured five more in attacks at three different clinics that provided family planning services.