The golden carp and the symbolic role that it plays in this excellent novel is of course closely tied up with religion, and so your answer to this question cannot avoid this. However, I would argue that the existence of the golden carp does far more than merely provoke Antonio to question Catholicism. It actually presents Antonio with a rival belief system that offers its own knowledge, wisdom, guidance and comfort. Let us remember that, in the novel, Antonio looks to Catholicism to answer his questions, such as why evil exists in the world. When the long-awaited first communion finally arrives, which, his mother promises Antonio, will answer all of his questions, Antonio hears nothing but silence. In the context of this novel therefore it is important that the golden carp and the alternative religion and belief that it represents is used to symbolise the way in which no one religious tradition is superior and has all the answers. Every religion has its own different, but equally valid, "story" of the world and lessons that can be learnt from it.
This is of course expressed most strongly by the end of the story, when Antonio realises he does not have to choose one or the other, but can actually draw from a number of different sources to establish his own identity and understand the world. Note how in Chapter 22, Antonio realises that the various competing opposites in his life do not need to be chosen between, but can co-exist:
"Take the llano and the river valley, the moon and the sea, God and the golden carp--and make something new," I said to myself. That is what Ultima meant by building strength from life.
Antonio thus is able to look towards the building of a "new religion" through the existence of the golden carp and the alternative belief system that it symbolises, "building strength" from the different elements of his life.