Yeah, recognizing what is "nice" and "nasty" has an instinctual component, and a cognitive component. The cognitive component depends on the model of the world, which is easily influenced by politics. For example, if someone honestly believes that gay people cause hurricanes, then opposing gay marriage is effective altruism according to their model.

The instincts are unreliable and can be manipulated. A person may be perfectly polite... and then go to their office and organize a genocide.

But I still think the instinctive part can serve as a sanity check. If someone pretends to be nice, and yet they miss many small opportunities to be nice, and are habitually nasty in situations where it doesn't serve any obvious purpose... then it's worth considering a hypothesis that this person actually is a nasty person who happens to belong to my faction. That their nastiness is not instrumental in fight against a greater evil, but it's who they are, it's what they enjoy doing.

Specifically: If PZ Myers wants to desecrate a catholic host not because he is an asshole, but because he honestly believes that it is instrumentally useful in creating a world where people are more nice to each other... then I would expect to find more evidence confirming that he cares about people being nice to each other. Until I get that evidence, I will consider "a person does X because they prefer doing X" my null hypothesis for human behavior.