It's a little more complex than simply determining whether one piece of legislation supersedes another. In short, the Equality Act 2010 does not provide immunity from prosecution for criminal behavior. If an individual is suspected of committing a crime, they can be prosecuted regardless of their protected characteristic (in this case, race). For example, if someone with a protected characteristic commits theft or assault, they can be prosecuted like anyone else.
While the Equality Act protects against discrimination, it does not prevent lawful prosecution. Where it becomes difficult for the police and the judiciary is when arrest or prosecution is challenged as being predicated on discriminatory motives. While I'm not privy to the details of this case, I'd like to think the police acted on prior intelligence about the motives of the group in question and were, therefore, confident that their actions were not liable to be challenged as discriminatory under the EA 2010.