I'm going to go out on a limb and say that it's Grace's blond friend, Sylvia(?) that did it. I think she was the "one other affair" that Jonathan referred to, and it has something to do with that. Because, otherwise, what was the point in bringing up that he had one other affair? Or, maybe Sylvia had an affair with Elena and was jealous, and killed her in a fit of rage, and then decided to frame Jonathan. She picked Henry up from school, didn't she? So she could have hid the murder weapon in his violin case. I haven't worked out exactly how or why, but I'm putting my money on Syliva.