I don’t know about the 1% figure, but King Tut lived over 3000 years ago and that’s a lot of generations. Ancient Egyptians had more interactions with people in the Levant. Modern Egyptians have more descent from Sub-Saharan Africa. Massacres aren’t necessary to explain the change. The history of the Coptic Christians also suggests that the change wasn’t brought about by exterminating the earlier inhabitants.
Typically, when a group has almost no genetic relationship to the previous group that occupied the area... something very unpleasant took place at some point, whether or not the events made it into the history books.
I know that Coptic Christians are Egypt's largest minority, and I know that they claim a close relationship to ancient Egyptians. But I have no idea if there has been any genetic testing to confirm this. The article that we are discussing makes no mention of this which would be surprising if the data existed.