What deems someone a winner is that the ref or the judges call it. You can certainly dispute the DQ, but people have disputed his win over Gustafsson as well (could certainly have been a loss if the judges called it like in some previous title fights), so that goes both ways.
In the end I think it's kind of irrelevant. Wins make you great, not avoiding losses. Jones has had a great run, and what he loses from being in a dying division (the regrowth of the old guard has not been great) he'll have a great chance of more than making up for at HW (granted not a deep weight class but he's stepping up).