This is simply understood as a dispute in girsaos. In terms of historically who said what, how could we know?
In terms of halacha, the Aruch LaNer ad. loc., and in his Bikkurei Yaakov 625:2, says that the definitive version is the one found in Sifra and Mechilta. This is how the Tur Orach Chaim § 625 could rule that the booths were the clouds of glory, being that we never rule like Rabbi Eliezer. The Aruch LaNer goes so far to suggest that the Tur must have had this version even in his gemarra. I suppose he writes that because he felt the Tur wouldn't choose a Midrash Halacha source over the gemarra. He also says the Rokeach cited the dispute this way. Perhaps this was enough evidence to suggest a variant version of the Bavli.
He also suggests that this is why Rashi explains the verse to be referring to the clouds of glory. Rashi must have had in his gemarra that Rabbi Akiva said it, and explained the verse according to the halacha.
I'll just note that according to the Hachi Garsinan database, all nine ancient manuscripts we have for the Talmud Bavli have it as we do. At the very least, you see the Aruch LaNer prefers the version found in the Sifra and Mechilta, otherwise he's at a loss to understand the Tur.