It seems somewhat bizarre an Equalities Act apparently enshrines religious privilege. However, I'm not entirely sure that is what the ruling means. I think the coroner has just been told she cannot reject religious reasons for expediting proceedings automatically. She has to give the same considerations due to any request. She's still allowed to say no.
In fact, reading between the lines, her motives may not have been entirely due to the cause of secularism. It looks like one particular religious group was applying unwanted pressure to her staff and she used the policy as a way to stop that.