Sure, but Ami has been getting killed the entire time. Ami should be first in his heart I agree, but I think he hasn't really seen her as a person until very recently. The thing that made Maya special to him is that she was existing on the same plane as him, i.e she was a constant and fully aware of the state of the world. Well that, and she was seemingly unattainable, which of course created a fascination. This allowed their relationship to grow slowly and naturally over the course of his "rebirth" so I understand why he would feel like he lost the one thing he cared about the most, because to this version of Sensei, he did care about her the most. Maya was the only one he saw as a human being the entire time, as opposed to all the other girls,including Ami unfortunately, who he saw as toys.There's not a single character but Ami that I can think of that could have made Akira react like this unironically.
In the totem pole of characters that could make Sensei be extremely devastated, I can see Maya being a runner up, along with maybe Ayane and Niki, making sensei very sad, but nothing warranting a full on mental breakdown.
Now should it have been this way based on things we know now about their relationship? Probably not but I think it's kind of obvious that Sel didn't plan every single detail of this story from the very beginning. And even if he did frankly, time changes you, the Sel who started LiL and the Sel writing LiL now are not the same. I know I'm not the same person I was four years ago.