Glad we are all in agreement about what this discussion is about. Now then, to the read discussion with proper arguments and stuff.
I think that reletively harmful acts of prejudice should be punishable when the prejudice leading to the action is more dangerous or harmful that the act would be by itself. For example, shouting verbal abuse at someone because of discriminatory prejudice should be punished more firmly than someone simply verbally abusing a random member of the public for shits and giggles. I understand that you might disagree with this but I think that hateful and unjustified bad actions are worse than just being a general asshole because it is fun.
However, this rule doesn't apply or is completely reversed in cases of really really nasty actions. I could use many examples but the most extreme that comes to mind is suicide bombings. Suicide bombers are generally horrible people who have misunderstood a religion or are completely deluded about what they are achieving in their actions. However, if you believe (however wrongly and ignorantly) that you are making the works a better place by killing innocent people then you are just confused. Although this is a terrible act it is much better than killing dozens of people for shits and giggles while being totally aware of the consequences of the crime.
I really, really don't want to link this with Islam but if I remember my primary school RS lessons correctly there is a message in the Koran which relates perfectly to my rule. It can be paraphrased into "what Allah cares about is the intention of the action, not the result." This is probably meant to mean that accidental harm is forgivable and thus acts of intentional violence are not forgiven unless it is completely necessary.
I hope this post makes enough sense to create a decent enough discussion. If you disagree please tell me using logical analysis rather than straw man arguments and hyperbole.