In addition, it is important to note that both Emily and Toby have only known the role assigned to them--she is the aristocratic and priviledged southern lady who is accustomed to servants. He is the servant and has been groomed for that purpose. Once Emily is dead, she no longer requires Toby's services. Emily is freed from her bonds, and likewise, so is Toby.
The black servant Toby signifies the vestiges racism of the traditional south that has its counterpart in the "lady" status of Emily. While racism results in a denigration of people for their color, the cult of the "lady" limited southern women to a different lack of power, as seen in the demise of Emily. It is appropriate that he leaves by the back door and is "not seen again" for this is the moment of Emily's death, when she is freed of the ideologies of being a lady that made her so unhappy during her lifetime.
I also think that Tobe leaves at the end because he knew about Emily's secret all these years and never told anybody...