So, if a Muslim baker refuses to decorate a cake with a caricature of prophet Mohammed, claiming it goes against his religion, he can be charged with discrimination on the basis of religious belief. That is the implication of the judge's ruling:

No it isn't. Have you read nothing leading up to this point? If the Muslim baker did as you suggest it would be fine. If the Muslim baker would not make the cake because the customer was Gay he can and should be charged with discrimination. The judge in the case in question believed the baker was being discriminatory about the plaintiff, not the message.