I found that scene to be strange, too. I went back thru her conversations with Lori. When Mare was released from the hospital, Lori tells her that Ryan told her that John was involved with Sandra again.
We know that Ryan never said those exact words; he let Lori believe that. When Mare confronts Sandra, John has already confessed to the incest with Erin, being DJ’s father and murder.
As you say, there is some ambiguity about when John stopped abusing Erin. If Mare made the assumption that John DID resume the affair with Sandra, it is because Lori initially believed - and comm