I would say hating someone due to their belief system would be far more logically and morally justifiable than hating them because of their race.

We can probably claim that a person's chosen religion would tell us more about an individual than what race the person is born into. Hence, if we happen to have a great dislike for that particular belief we could logically infer that we do not like this person because 'he believes and follows something I hate'.

It isn't really important if it involves torture of children or baptising children. That would just be an argument that 'justifies' the original question in light of typical everyday western values. What logically matters is you base your hatred on knowledge of what the person believes in, not prejudice of what the person may be.

On the other hand, in practical everyday life we all known hatred due to religion and hatred due to race mostly go hand in hand.