The question of the thread is extremely complicated, relying on definitions of religion, empathy and kindness which must be difficult to tie down. Not to mention that indoctrination is a pejorative from the start. That’s before you even get to methdology, reliability, replicability and so on.
Studies such as these are next to worthless it seems to me, being pieces of rhetoric rather than genuine contributions to knowledge. But then I consider most contributions to knowledge suspect on some level. From that perspective at least one could say that the flaws of this particular piece at least have the virtue of being readily apparent. More sophisticated kinds of evidence are often proferred but are not less faulty if one has the ability and care to take them apart. What can we really know about ourselves and the world when it comes down to it? On a practical level we take much for granted, and it is only reasonable to do so. But fundamentally, how many things do we really know for certain? Not a lot. So I think it’s incautious to make general statements on such sweeping issues as whether children of religious parents are more empathetic.