Your question assumes R' Yehuda's opinion is rejected. If you look again you will see that is not the case. Rather, the gemara is using R' Yehuda's opinion to disprove a historical statement of R' Yochanan. R' Yochanan claimed this Mishna is only according to R'Akiva and not the Chachamim, but since R' Yehuda referred to this ruling, and he cannot have meant R' Akiva's position, he must be referring to the Chachamim.
Now you could ask, maybe he is not referring to anybody's opinion, just stating his own? But there are two reasons why that is not what R' Yehuda's statement sounds like:
First, the use of the word "אימתי/when was this said" implies R' Yehuda is clarifying an existing opinion, not stating a new one.
In addition, as a general rule, there is a difference between אמרר'פלוני and ר'פלוניאומר. The latter is used to imply that ר'פלוני is disagreeing with the previous statement. Since here the braisa says "אמרר'יהודה", it implies he is not arguing, just clarifying.
In fact, the Rambam actually does rule like R' Yehuda, so his opinion is not rejected at all.
