In my interpretation of the lyrics, he is wrestling with forbidden love but not the love for a nun as many have thought. He has fallen in love with his half-sister whom he has been introduced to but didn't know she existed prior to some broken family interaction along the path of his life, hence the surprise. She also has shown that she felt something more than sibling love for him during family gatherings. He tries to fake being a brother but he is tortured by his lust for her and prefers to stay away from family contact for fear of being taken as a family member by her and lose his chance with her. Not ready for the alter would mean that marriage is not an option due to his blood ties to her, but that he seeks to live his life with her anyways as.
This song is about a letter he writes to her after years of painful waiting for her to catch up to him in years and reach adulthood, and to see if they can move on without one-another, metaphorically, Sunday but then Monday means several painful years of questionable, cautious, cat-like commitment to being there right when she's ready. Originally, the lyrics said Meet me in VA would have meant giving him her virginity but as