He is part of the clan, but like with Eleanora, kinda loosely affiliated. 

So when she was a new vampire, she was really wild, right? She fed whenever she wanted, on whoever she wanted. I figure, giving her inexperience, she probably accidentally turned several of her victims. So we got several men across town turning into vampires, which is really bad, and even worse, one of the men Nadya turned was the husband of one of Eleanora's human friends, which means Eleanora and therefore Jonathan are way too close to it and can easily be suspected. We all know that wouldn't sit well with Elizabeth. 
So everyone in the Mercer clan except Jonathan has to clean up this very dangerous mess Nadya made and consider immediately leaving town.