I think ROTJ:R is definitely an edit that would benefit from an alternative 'purist' version viewable via a branching disk.

That way if, as I suspect, the ST only makes specific references to events or surviving characters from the OT, the purist cut doesn't affect continuity with these new films as it will play out as it did before on a story level.

The reason I suspect the ST will not make any references specific enough to the PT to impact continuity with the PT:R is that I think Disney are well aware the prequels are best left forgotten and also the events in the prequels occur before the lives of anyone in the story anyway so it's not likely to be referenced in the ST regardless - unless they start talking about specifics like midichlorians or Anakin turning to save his wife from dying during childbirth etc.....in which case I'd day the ST is doomed anyway as they'd clearly be following the George school of expository dialogue.