It's canon in the show that Stephen and Charlene are cousins! Stephen describes his family tree as "having so much intermarriage it looks like a Brillo pad," so he thinks a romance with a (female) cousin is a perfectly reasonable goal.

Their relationship in this AU gets expanded on a lot in the next book, State of Grace. Their new dynamic has a nice balance: Charlene provides Stephen with bearding and childcare, Stephen provides Charlene with income and a place to live. As kids they were really close in a platonic way, and they're trying to rebuild that friendship.