“Bar Kochba and his war happened hundreds of years before the mention of “shlosh shevuos” in Ketubot.”
The drasha from Shir Hashirim predated Rabbi Akiva. The Targum Yonatan ben Uziel (who lived before Rabbi Akiva) mentions the Bnai Efrayim. I don’t have sefarim with me now, but look at the passuk mentioned in the sugya in Ketubot. The Targum Yonatan is on that passuk.