On a previous talk, he advises Akira to not open his eyes until it is done. Now, here's my question, if Akira had sex with Maya prior to this wouldn't he have erased himself regardless? As it happened so many times before, according to Maya? So why does a god even have to be involved in this?
We can only make guesses, this theme tied up with speculations and shizotheories. I can build an answer on one of them.
1. Maya is a shrine maiden of an old god (named with letter "T"), and from the very beginning she served her god faithfully.
At some point she falls in love with Akira (who is most likely also part of the dynasty of deities) and stops believing in her god.
The old god dies, since gods in whom people do not believe cannot exist.
2. A bunch of new false gods appear and replace each other. At some point they decide to resurrect the old god, the details are not important now. Some condition must be done for the resurrection of the old god - for example, impregnate everyone or climb to the top of the hill of naked bodies, doesnot matter now.
3. The current iteration of Akira is different from previous ones - and apparently, it is best suited to fulfill this condition.
It is impossible to return Maya back to her god, especially considering the “real sensei”, she will only get in the way.
Accordingly, the easiest way - to erase her.