One way around the Vader being the father of Luke but also the murderer of Anakin would be to seperate the two characters.

Obi-wan had a friend called Anakin and a former pupil called Vader.

If Anakin killed Vader and took over his persona you could have both ideas reconciled.

Obi-Wan could have been lead to believe that his friend was killed by Vader when in fact his former pupil was killed by his friend.

It would make ROTJ a bit more complicated but it could have saved the prequels especially if Vader was already wearing a mask before Anakin killed him.

The volcanic confrontation between Vader and Obi-Wan in the prequels would still have the preserved surprise for people watching the series from 1 to 6.