Just because the court system currently does it does not justify the practice. I'm not a believer in thought crimes.
It's not a thought crime. It's an action, like firing someone for example, with a certain mental state attached. Pretty much all crimes require a certain mental state. If courts couldn't make findings on mental states you couldn't have the legal system.
From the Oxford English Dictionary:
Thoughtcrime
noun
an instance of unorthodox or controversial thinking, considered as a criminal offence or as socially unacceptable.
If someone decides not to hire a black because they are black, any charges against them are clearly thought crimes.