I think the easy, non-asterisk solution to this is to simply refer to the AL home run record. That way, we don't have to adjudicate who the "real" home run champ is; there's the NL/MLB record holder, and if you believe that record is tainted, there's the AL record holder.
That's what is going to happen, but the argument will only intensify if he does hit 62. It will never go away and as long as Judge doesn't pull a Chris Davis and continues his succesful career while Sosa, Bonds and McGwire are rejected from the Hall, I think most fans will side with Judge.
In the end, it doesn't really matter because it's just an opinion.