That article presents a very unsophisticated interpretation of the Pope's statements that fails to take account of much liberal theology since, oh, I don't know, 1850 or so (maybe sooner; I'm a little rusty). I haven't seen the full context of the Pope's statements, but I would assume the ones quoted in the article are juxtaposing (1) both (a) a philosophical conception of god (god as hypostatized "divine being," "unmoved mover," the "good") and (b) a rote interpretation of the Bible from a literalist standpoint with (2) the God of Christianity as understood by much modern theology (at least since Kierkegaard), which tries to divorce Christianity from philosophical (and particularly, Greek) thought and which recognizes that the creation myth was never meant to be taken literally and is thus fully compatible with whichever direction science says the wind is blowing today.
I'm not a Pope watcher; maybe this is a bombshell coming from him, but statements like these aren't new or unique to Christianity by a long shot.