First it helps to know that Magdalena is about his mother, a deeply religious woman who suffered a stroke that left her near helpless. Despite this, she remained faithful. He was angered by the idea that God allowed her to be struck down like that and it showed in the song, as he rejected her faith completely. I think this song is his own, as he tries to reconnect with God, wanting to accept and understand and both forgive and be forgiven his doubt.
DOH!! Judith, not Magdalena... Bit of a whoops there. Juuussst a bit.