I think it may be wrong to label this an "anti-theist hate crime," especially in the light that he probably did not know for certain their religious beliefs. I would venture to guess racial stereotyping and prejudices played a role in this (i.e. If George Zimmerman were an atheist, he'd still have followed and killed Trayvon due to racial stereotyping). I would also venture to guess American gun culture played a role in this (he was big on the "2nd Amendment" and the NRA's rugged-American "here's a gun, solve your problems" mentality). But, at the moment all we have is an anti-theist that committed a crime, and not necessarily because he was an anti-theist.
I belabor the point, but I am an anti-theist who believes all religions are dangerous, manipulative, power-hungry, and stupid. So, I'm probably a tad bias. But, I still see other parts of the kyriarchy playing into this more so than anti-theism.