The biblical references are the most blatant, and are definently within the movie. It doesn't take much analytical skill of knowledge of philosophy to find those ones. No one will argue the religious aspects of the movie.
But there are far more allusions within the movie than just the Christ/biblical references, and they all coexist within the movies. To claim that the movies are about one or the other would be incorrect.
The theories above to not rule out any sort of biblical allusions at all. They explain a possible plot point, but the biblical allusions exist seperate from whatever reasonings that you deduce Neo is doing what he is doing, just as the Eastern and Western philosophy exists seperately from the biblical allusions.
