My guess is somebody clued them in that if they didn't hit this guy with a hate crime then there would be precedent to protect people from hate crime status for crimes against Christian property.
That's not really how precedent works. Not choosing to charge him with a hate crime would be a matter of prosecutorial discretion, and wouldn't affect other prosecutors' charging decisions.
You better believe if you took a shit on whatever jeebus monument they have at the Mississippi Capitol they'd put you under the jail with every imaginable charge.