So at the end, it appears Castle is going to tell Martha (and Beckett since she's there) about his father. Do think he'll mention that his father was behind the death in the farmhouse? While the Castle family is forgiving, I don't see Beckett intentionally giving a murderer a pass.
But knowing how smart she is, she will probably figure it out once she hears the story. But by the time Castle and Alexis got home, the whole affair probably got a CIA cover-up.