Let me address Rav Saadyah Gaon’s פירוש first. The מגיה is called Moshe Zucker; as far as I know he is considered reliable. He shows very clearly which words survived in the Arabic manuscript and which he adds in himself. There are only a few words missing in this piece. And Zucker is very reluctant to say that Rav Saadyah was referring to רבי יוחנן, because (as you say) the phrase אחד מאומתנו seems quite disrespectful in tone. He tries to suggest an alternative, that the reference is to the kusi in the Medrash you quoted, but this doesn’t work because the kusi held that only Har Gerizim wasn’t flooded, but the rest of Eretz Yisroel was. He therefore concludes על כרחנו עלינו להשלים עם העובדה שהגאון מתח כאן את בקורתו החריפה על מאמר אגדה של חז”ל.
Now, what I imagine happened is that the Ibn Ezra (whose פירוש is largely based on Rabbeinu Saadyah Gaon) saw this piece in Rabbeinu Saadyah Gaon and assumed he was talking about a Karaite, because (as Zucker points out) the phrase אחד מאומתנו in Rabbeinu Saadyah Gaon’s פירוש usually means he’s talking about a Karaite. The Ibn Ezra probably didn’t know the Gemoro in Zevochim (the Maharshal you mentioned is happy to accept the possibility that he didn’t know Shas) and therefore rejected this פשט with language one expects him to use when talking about the Karaites. And again, the Avi Ezer understands the Ibn Ezra to be referring to Rebbi Yochanan, and struggles with the lack of respect.
I don’t see the psak of the Oruch Hashulchon as binding, and I feel able to argue with him. He is actually one of the ספרי הלכה I use most, but that doesn’t mean I accept everything he says. (I imagine that neither do you.)