It's sad and funny that the New York Times links in its article to a BibleHub online Bible of Deuteronomy 20:17, which the King James Version reads, "But thou shalt utterly destroy them; namely, the Hittites, and the Amorites, the Canaanites, and the Perizzites, the Hivites, and the Jebusites; as the LORD thy God hath commanded thee." God commanded Israel to destroy them, but in very ancient news, Israel didn't obey. Just because God commands something in the Bible doesn't mean that everyone does what He says. The Bible isn't the story of a people who were completely obedient, but the story of sinners who, even though God gets it entirely right, themselves get it usually wrong.
The science part of the study appeared in the American Journal of Human Genetics. It should be a great testimony to the authenticity of the biblical record, since it says that these people existed. Instead, many used it with great glee as a basis for the Bible not being true. This included The Telegraph, The Independent, The Daily Mail, The Tech Times, Mother Nature Network, Cosmos, and many more. They are saying in essence, "The Bible says they were destroyed, and they weren't!" The Bible says that God told Israel to destroy them. Israel didn't. As a result there was all sorts of Canaanite false worship in the land.
Joshua 17:12, Judges 1:27-28, 31, and 2:3 read (some underlining for emphasis):
Yet the children of Manasseh could not drive out the inhabitants of those cities; but the Canaanites would dwell in that land. . . . Neither did Manasseh drive out the inhabitants of Bethshean and her towns, nor Taanach and her towns, nor the inhabitants of Dor and her towns, nor the inhabitants of Ibleam and her towns, nor the inhabitants of Megiddo and her towns: but the Canaanites would dwell in that land. And it came to pass, when Israel was strong, that they put the Canaanites to tribute, and did not utterly drive them out. . . . Neither did Asher drive out the inhabitants of Accho, nor the inhabitants of Zidon, nor of Ahlab, nor of Achzib, nor of Helbah, nor of Aphik, nor of Rehob. . . . Wherefore I also said, I will not drive them out from before you; but they shall be as thorns in your sides, and their gods shall be a snare unto you.Scripture itself later says the Canaanites were not destroyed from the face of the earth, which was the point contradicting the New York Times and all the other fake news.
I guess we can wait for a retraction. You should be heartened though. Those on the other side are wrong again and obviously so. They are either totally duped or deceived or rank liars, but they are wrong. This is just who they are, so don't let them bother you.