According to the contemporary scholarship, even though modern Orthodox Judaism follows matrilineal descent, there is evidence to suggest that this was a shift that occurred during the second century, and that pre-diaspora Judaism was patrilineal (Cohen, 1985). There are of course, other people discussing this although not necessarily in the same way as Cohen did (Heger, 2012). Outside of scholarship, others offer examples and arguments such as saying that "the oldest historical way of identifying Jewishly was through the father. Just look in the Torah. Who is Jewish? Moses is Jewish, but his wife is not. Would anyone say Moses’ grandchildren weren’t Jewish? Of course not. What a crazy thought! What about King David? According to Jewish tradition, one of his descendants will be the messiah — not a descendant of his wife. Would anyone today say HIS children aren’t Jewish? Of course not! So, why then, would we say that the child of a Jewish man living today is not Jewish, if that person is choosing to identify Jewishly?" and "the shift from patrilineal to matrilineal descent happened around the year zero" and that the Rabbis encouraged the exclusive-matrilineal system in order to discourage conversions due to Roman persecutions.
Others also say things like this: "Many people mistakenly believe that the criteria were laid out clearly at Sinai and have ever since been based on matrilineality, but that doesn’t seem to fan out with biblical and historical texts. This is also essentially baseless as no Mishnaic or Talmudic texts claim matrilineality to be a tradition from Sinai." and also "While it cannot be stated with certainty, it does still seem that Jewishness was determined by patrilineal descent even after Sinai into the biblical era. The Israelites were essentially the “sons of Jacob,” known as the 12 tribes of Israel. Tribalism was defined by the father’s tribe (l’bet avotam – Num. 1:2) since in those times the wife would join the husband’s household. Perhaps the most explicit verse referencing patrilineality is from Ezra 2:59 (also in Neh. 7:61) “The following were those who came up from Tel-melah, Tel-harsha, Cherub, Addan, and Immer—they were unable to tell whether their father’s house and descent were Israelite.”
King Solomon is said to have married foreign women of all stripes. If we take the biblical number literally, he had one thousand wives and probably thousands of children as a result. These children, of non-Jewish mothers, were absorbed into the Israelite community with King Rehoboam also being the son of an Ammonite wife of Solomon. This would suggest patrilineality in this era. It is unlikely that these wives of Solomon converted, since they were pagan-worshippers and eventually caused Solomon to stray from God (I Kings 11)."
Some even say that the Talmudic attempt at providing evidence of matrilineal descent tracing back to Mt. Sinai is unconvincing: "A number of verses are cited by the Talmud (B. Kiddushin 68b) in an attempt to show that the matrilineal principle has Biblical origin, but from a historical perspective none is entirely convincing." along with "Indeed all evidence points instead to a strong patrilineal principle." and "We have seen that there is no explicit ‘matrilineal principle’ in Biblical or Rabbinic Judaism. Rather Biblical and Rabbinic Judaism (and even proto-Christianity) consider patrilineal inheritance to be the proper way for a Jew to receive their status".
All this is quite problematic because to follow a matrilineal principle for something as important as Jewish descent is to a) possibly overrule a G-d's word and b) claim that what the sages taught was highly incorrect in halachic matters.
One solution is to push the Numbers Rabbah 13:15-16 and say that there are 70 different ways to interpreting the Torah ("Shiv'im panim la-Torah", basically meaning something like "70 faces of Torah"). Since research shows that matrilineal descent is a late Rabbinic post-exile invention, and is not necessarily from Mt. Sinai directly, then one can also use this principle of 70 ways of looking at the Torah to also interpret the heredity of rules to also work for both matrilineal and patrilineal descent. This is the only solution if we don't want to open the can of worms and say that the sages were wrong with such an important halacha or could completely overrule a Divine decree. In this way, we can say that its okay to follow patrilineal descent, but it was superior to follow matrilineal descent especially in times when it would be uncertain if the father was Jewish, so the Rabbis were merely shifting focus rather than throwing overruling G-d's Divine Law.
This is also not to mention that there are certain groups of Jews, such as Kaifeng Jews (who were formed as a Jewish community in China during the Song Dynasty, sometime between 960 and 1279 CE), who traditionally (particularly early on) follow the patrilineal descent of Judaism despite having both the Tanakh and the Talmud. There were "Kaifeng Torah scrolls" whose content is identical to the mainstream Torah. They followed all the standard Jewish practices like abstinence from pork (rare in Ancient China), circumcision, and more. Unfortunately by 1800s, they were completely unable to read their texts with their last Rabbi dying in early 1800s and the community being fully integrated into mainstream Chinese culture before emerging back today. According to (Xu, 2005), there is evidence to suggest that the community did have a Talmud. Despite all this, they somehow understood that the proper halachic way is to follow the patrilineal descent according to their interpretation of the scripture.
Is there any other way to reconcile the evidence to suggest that the original Jewish practice was to follow patrilineal descent according to research, and that some Jewish groups interpreted traditional scriptures to follow patrilineal descent and that mainstread "Rabbinic" Orthodox Judaism today follows matrilineal descent?
EDIT: As a note, I'm not presenting a doctoral thesis in the question, I am saying that there is evidence suggesting patrilineal descent for early Judaism and even some post-Talmudic Jewish groups, and I presented some of the scholarly evidence here, and based on that, I'm asking how to reconcile that with the mainstream understanding of halacha.