It is truly sad to see such anger and hostility within a family; for a parent's last words to be “I never want to see my child again” is truly heartbreaking.
Nevertheless, a few thoughts:
Whatever might have been, it is now done. They are buried side by side, and you had no part in arranging this. It is out of your hands at this point.
We deeply believe that when we die and leave this earth, our souls (the real us) goes to a place where Truth and Peace reign, and where we are freed from much of the confusion that hindered and blocked our vision in this world. I have often had the occasion to say to someone, “Now that your father is in Heaven, he can finally appreciate who you are and the kind of person you have become, unblocked by his small-minded biases while he was here on Earth.” Obviously, there were many hard feelings between them, and I have no idea what caused those feelings. I do know, however, that more often than not, broken relationships can be mended if one side or the other would be willing to look beyond the initial cause of bad feelings and look at the broader picture. In Heaven, both of them will be shown the whole picture of whatever happened between them, and hopefully, after seeing the totality of everything that went on during their lifetimes, they will find a way to put the past behind and not be stuck in the tzuros that kept them apart in this world.
It may sound trite, but your father got his wish. He never saw her again (in this world). Hopefully his wish will have been considered complete in this world, and not extend to the next.
I do not see any positive purpose in erecting a shed or inscription or anything else that will call attention to the dispute. No one else needs to know about this. They are both gone now, resting in peace. I would just leave it as it is.
May you find comfort in mourning them, and may the One who makes Peace on High, make upon us and all of Israel, Amen