Greetings. Recently I was reading some interesting discussion that DNA tests done on members of the Samaritan population show that they share identical DNA with Jews. If this is the case then we would have to say that in the first instance the Kusim discussed in Sefer Melachim and Ezra who were brought in from Asia are not the same people as the Samaritans. And no mention of Har Gerizim is mentioned in Nach. So the connection made in the braisa in the name of Rabbi Akiva making the Kusim of that time the descendants of the original migrants would have to be incorrect. If so, then the picture changes. The original migrants somehow disappeared, and it was Israelites who affiliated with Har Gerizim as an alternative to Yerushalayim. The big question then would be: why did Chazal identify the people at Gerizim as descendants of the migrants if they were actually from the Shevatim (even if some had intermarried), even if the term Kusi was a pejorative nickname? One would imagine that the true identity would have been hinted at.
David Goldman
I did some peripheral internet research on what you mentioned. With my little understanding of genetics I can still understand that the male Samaritans have similar DNA to Jews but the females do not, suggesting that they descend from male Jews who intermarried with foreign females. The Assyrians were known to move populations around in order to mix and dilute the national orientations, and this people-shifting may have led to Jews marrying Assyrian women and returning to Samaria after it was left desolate. These Jews practiced a form of religion but were influenced by their Assyrian sojourn, hence the foreign deities served by them as well as serving Hash-m. The practice of sanctifying Har Gerizim might stem from the time when they did not go to the Temple during the period of the Israelite kingdom.
Ezra may have identified them as Nochrim because they married Nochri women and cast their Jewish lineage off, but technically they were Jews who had left their Jewish traditions behind after the exile in Assyria.
I noticed your question is discussed in this reference: https://judaism.stackexchange.com/questions/31093/ezra-claimed-that-samaritans-are-not-jews-is-genetic-data-in-conflict-with-this
Yoel Domb