No, it's because the appendix said he had a male lover,
The appendix was published two books after Inrau and Proyas first come to our attention and was referring to his room mate (Sancla) when Akka was in school. No one who thinks Akka diddled boys formed that suspicion only after finishing TTT.
his disproportionate reaction to inraus death,
You're projecting into the event. Akka loves Inrau because he sees in Inrau the innocence and cleanliness of heart that he knows he has lost:
Inrau . . . For Achamian, to think this name was to know peace for a fleeting instant. He had known so little peace in his life. And now he was forced to throw that peace onto the scales with terror. He must sacrifice Inrau in order to answer these questions.
Inrau had been a coltish adolescent when he’d first come to Achamian, a boy still blinking in the daybreak of manhood. Though there had been nothing extraordinary about his appearance or his intellect, Achamian had immediately recognized something different about him—a memory, perhaps, of the first student he’d loved, Nersei Proyas. But where Proyas had grown proud, overfed on the knowledge that he would someday be King, Inrau had remained . . . Inrau.
Teachers found many self-serving reasons to love their students. More than anything, they loved them simply because they listened. But Achamian had not loved Inrau as a student. Inrau, he’d realized, was good. Not good in the jaded way of the Mandate, who trafficked in the mire as did all other men. No. The good he saw in Inrau had nothing to do with kind acts or praiseworthy purposes; it was something innate. Inrau harboured no secrets, no shadowy need to conceal faults or to write himself large in the estimation of other men. He was open in the way of children and fools, and he possessed the same blessed naïveté, an innocence that smacked of wisdom rather than ignorance.
Innocence. If there was anything Achamian had forgotten, it was innocence.
Remember how much self-loathing he has while he is in Sumna and hears the pilgrims going on about how sorcerors are a cancer? He is more than a bit tempted to agree.
If that's not enough to convince you that this wasn't about Akka having mad lust for boy anus, consider that the self-characterization implied in the above reminiscences, i.e. that Akka is a teacher and sees himself as such above all else, is also
exactly how Kellhus reads Akka's character and manipulates him into giving up the Gnosis. There is no trace of Kellhus seeing anything erotic in Akka's relations with himself, Proyas, or anyone but Esmi.
the disproportionate reaction of house nersei of breaking a centuries long contract with the mandate because of the "official" explanation of a teacher uttering a minor blasphemy (especially when the teachers very existence is 1000 times more blasphemous),
That could be a pretext for anything, and is itself disproportionate with the alleged crime. To reiterate,
you don't buttfuck the king's son and then just walk away, especially when the King and all of his nobles, including the older brother of the boy you touched (Proyas is the king's second son, and only became heir apparent on his older brother Tirrumas' death in 4100) all have Chorae. We saw clearly that sorcerors could be trapped and tortured Akka when he went to the Sareotic Library, there is no reason to believe he would be any less easy to bring to heel when every caste-noble in Conriya with a Chorae is after him for rape.
It is worth noting that Akka's successor (Charamemas) was a Shrial priest and famed scriptural commentator; that fits neatly with the official stated reason for Akka's dismissal: unorthodoxy.
and because akkas rivals directly accuse him of it.
The most trustworthy of voices? There is no reason to believe that their accusations were chosen for truth, as opposed to usefulness to the accuser. This can be seen even in the real world: want to ruin a teacher, accuse him of pedophilia. Often merely sowing doubt is enough. A man's enemies are not a reliable source for information about his character.
And given the immensity of their accusation it is fascinating it is the only slight akka suffers in five books that he does not ruminate and brood on for multiple paragraphs, his only thought is basically shock that they knew the best way to wound him.
He's shocked that they know what he loves most: teaching. Akka's enemies took the accusation of pederasty as a potent way of slurring his character; Akka took it to heart because his character
as a teacher means something deep to him, and he is surprised that they knew this (if they did, to me it looks like they just used whatever slur seemed most dangerous given his situation and accidentally hit a nerve in terms of his real personality).
It is all suspicious at the least.
It is suspicious, and Bakker may intend for us to think it that way, even if he just wants to play a game and Akka isn't really a boy-toucher. But there is nothing approaching a slam-dunk in the text that would prove this. I think Bakker is teasing us.