In theory, this version of Sensei being erased might even benefit Makoto.
Considering that, like Maya Prime, Ayane and Makoto can make it to the roof, then even if Sensei doesn't, they could probably just seduce the next version of him. New Sensei probably wouldn't remember Maya Prime, and presumably the rest of the class would be reset as well, getting rid of the harem.
Then they'd just have each other to worry about, and well, Makoto's likely already thought this far ahead hence the whole betrayal stuff:
Ayane has probably realized this as well, but doesn't want to admit it. It was implied quite a bit that she wanted to take Maya's place throughout Chapter 3:
And for all we know, she may have played a part in what happened to Maya Prime.
Unlike Makoto though, I don't think Ayane would be able to handle Current Sensei being reset. Just finding out Current Sensei didn't remember her before Chapter 1, made her consider mental suicide:
Kind of sucks that only straight monoamorous girls have apparently got to the rooftop so far. A "there can only be one" outcome seems inevitable.