The objective of a hate crime is to target not just the immediate victim, but also others of the same race, religion, sexuality, etc. In other words, if Corporon's father and nephew, as well as the other victims, were killed specifically because they were Christians, it absolutely was a hate crime and needed to be prosecuted as such. Was the perpetrator's objective simply a mass killing (something already far too common in our society), or was there an additional motive of terrorizing Christians? Since he reportedly intended to kill Jews, there's already good evidence that he was targeting a specific group, so the implication is there.

Hate crimes can be pretty hard to pin down, but they should be investigated where evidence exists because often there is an underlying wish to inspire others to engage in the same sort of actions. What perpetrators want is the targeted group to live in fear. No one should fear for their lives because of their race, religion, sexuality, etc.