In their article, “Siddur Avodat Halev: A New Siddur and Insights on the Old” (Hakirah 28, Spring 2020), authors Aton Holzer and Arie Folger “suggest that the three she-lo asani blessings … are a polemical response against that Christian doctrine, providing the added benefit that a closet missionary serving as a shaliah tzibbur could be uncovered right at the beginning of Shaharit, long before he refuses to recite Ve-lamalshinim” (p. 56).
Evidently, the authors imagine that our present custom of the prayer leader (sheliah tzibbur) reciting the Birkhot ha-Shahar in the synagogue, dates back to antiquity. The truth be known, this is a later innovation. In the period of early Christianity, when the objective of Hazal was to ferret out crypto-Christians from serving as prayer leaders, it was the custom for the individual to recite these blessings in the privacy of the home before arriving in the synagogue.
Maimonides mentions our custom of reciting the series of blessings (that have come to be known as “Birkhot ha-Shahar”) in the synagogue and writes that it is mistaken (MT, Hil. Tefillah 7:7-9). In a responsum, his son, Rabbi Abraham Maimonides, writes that he succeeded in abolishing this erroneous custom of arranging the blessings in the synagogue (Teshuvot Rabbeinu Avraham ben ha-Rambam, ed. A.H. Freimann and S.D. Goitein, Jerusalem 1938, no. 83). (Parenthetically, Rabbi Abraham Maimonides attributes the shift in custom from individual to communal recitation of the blessings, to Rav Hai Gaon and Rav Sa‘adiah Gaon.)
Despite valiant efforts on the part of the Maimonidean dynasty in Egypt to restore the original Talmudic custom, by the time of the Shulhan ‘Arukh, the custom of arranging the Birkhot ha-Shahar in serial fashion in the synagogue prevailed. After recording the original custom of reciting the blessings piecemeal in the home, Rabbi Joseph Karo concludes: “And now, since the hands are not clean, and also because of the ignoramuses (‘amei ha-aratzot) who do not know them, it is the custom to arrange them in the synagogue …” (Shulhan ‘Arukh, Orah Hayyim 46:2). The author of the Shulhan ‘Arukh has essentially transcribed the language of Rabbi Jacob ben Asher (Tur Orah Hayyim, chap. 46), which is a bit more explicit: “According to the order of the Gemara, it was fitting to bless each at its time, [yet] as the hands are not clean, they enacted to arrange them in the synagogue, and also because of the ignoramuses who do not know them, they enacted that they arrange them in the synagogue …”
As for the paradigm shift that reportedly took place in the days of the Ge’onim, I think it more reasonable to ascribe it to the phenomenon of widespread ignorance (‘am ha-aratzut), as did the Tur, rather than to the challenge of Christian intrigue.