A child of a Ger is not necessarily a Ger, so there is no proof from Rebbe Akiva. Shemaya and Avtalyon might have been children of Geirim and not Geirim themselves. B’nei Banav Shel Haman, even if we are talking about the Geirim themselves, were not necessarily in a position of authority. There is nothing wrong with a Ger teaching Torah.
I remeber the reason being that it is uncomfortable for people to be judged by a newcomer. If the people consented then it is OK. That is why if someone was voted in there is no problem. Tosafos says this regarding Devora.