First of all, it’s evident that people often have unconscious motives for their actions. For example, parents “wishing the best” for their children can act out of frustration about their own past failures. So it’s likely that some acts of discrimination are based on similar “deep” motives. Some of us who genuinely believe that we are colorblind may still avoid black neighborhoods at night, cross a lonely street when a tall black male comes our way, or favor a CV sent in by someone with a “‘Caucasian” name. Tests have shown that people are more biased than they admit to themselves.
So we may be violating anti-discrimination laws without “really” and consciously wanting to. You could say that in such cases we shouldn’t be prosecuted for breaking the law, because there is no intent on our part. Discrimination takes place but no one really wants it to take place. True, normally there’s an intent requirement when deciding liability: if you drive your car and you hit someone who crosses the road where he or she shouldn’t do so, you’re not criminally liable. You killed a person but didn’t intend to. In some cases, the lack of intent diminishes rather than removes liability: if you’re in a fight with someone and the other person dies because of your actions, you won’t be charged with homicide but with the lesser crime of manslaughter if you didn’t intend to murder.
As the example of manslaughter already makes clear, intent isn’t always necessary for liability. Hence, lack of intent can’t be the reason not to make unconscious discrimination a crime.
Anyway, intent or the absence of it is often very difficult to prove. In the case of homicide/manslaughter, you can use witness accounts or physical evidence, you can reconstruct the crime and try to figure out if the killing was planned or intended, or you can interrogate the perpetrator, and even then it’s rarely easy. Things seem to be much more difficult still in cases of unconscious discrimination. Looking for intent is basically trying to look inside people’s minds, which isn’t obvious, and when people fool their own minds it’s becomes even harder.
If we accept that unconscious discrimination should be a crime in certain cases, and perhaps equivalent to conscious discrimination, then the problem is how to prove that it took place. In the case of conscious discrimination, you can often rely on the utterances of the person(s) who discriminate. That’s evidently impossible in the case of unconscious discrimination. Perhaps you can’t prove it in individual cases – if one black person’s CV is rejected, it’s probably impossible to say it’s because of implicit or unconscious racism. However, if a company rejects a large number of such CVs, and correcting for other factors such as education or skill level doesn’t remove bias in the distribution, then you may perhaps have evidence of discrimination (that’s a technique that’s useful in cases of conscious discrimination as well, by the way). So you would need to rely on statistical analysis, something that usually isn’t done in the determination of criminal liability. It’s not because x % of all killings are manslaughter that everyone charged with a killing has x % change of “getting away” with manslaughter. The decision to sentence someone for the crime of murder or manslaughter is always made on an individual basis and not a statistical one, although past conduct of the suspect can sometimes come into play.
An additional difficulty: if we accept that laws aren’t only meant to punish but also to prevent and deter, it seems that the latter goal is futile in the case of unconscious discrimination. People who are not aware that they engage in discriminatory activities will hardly be persuaded by laws telling them to stop doing so.
I’m personally not yet ready to take a firm position on these issues. For more information on this topic, take a look at this interesting paper.