Didn't the Producer of AKB know about Minori's real identity too?
He could work with his relationship to hide his true gender.
That's the thing - yes, despite the former senbatsu lead Maeda and Akimoto himself knowing the secret already, the fans would surely react otherwise. The power of the people is more powerful than the administration (or the elite like Aphrodite, Okabe's mother)...and then there's the girls themselves: the kenkyusei that he met, the real life personalities, imagine how the girls would react if a guy was with them all this time...
Imagine how AKB would collapse even with Akimoto's protection...especially also since Minoru as Minori crafted a highly influential character as an idol.