ROB,
In a 1998 Shabbos Purim drasha in the YU dining hall, R’ Schachter, in a diatribe against the Orthodox left, said that R’ Saul Berman and Edah(the now-defunct vanguard of liberal Modern Orthodoxy, which was absorbed into YCT) was “a sort of internal Amalek.” Rabbi Berman, at the time, defended the remark as a kind of extreme rabbinic poetry, although he’s since rethought the matter.
I also read that in the 1920s, the Rebbe of Munkatch labeled as an Amalek none other than Agudath Israel, which he thought was a bunch of crypto-Zionists and modernizers.
This is nothing new under the sun, and leaders within the realm of YU/RCA are guilty of it themselves.