Yes, it's missing crucial works like Cur Deus Homo and On the Incarnation by St Athanasius as well as some of the ones you mention, but I think some of those are in the curriculum if you look a little harder. One needn't be a Christian to benefit from such works; they are foundational to Western civilisation.
Confessions is on the program Sophomore year, as are excerpts from Summa Theologica. I vaguely remember one of the differences between the campuses being that Annapolis students read some Calvin and Santa Fe students read something else, but I don't remember what it was.