I think Ella's the most complex character in the game currently.
By that I mean, writing-wise. I think she is, as of now in v0.881, the character with the most depth to her writing. No saying others are shallow. But the fact she's basically the front and center when it comes to WeirdWorld (a lot of stuff ends up tying with her one way or the other, she has a huge place in the story, WW uses her as avatar... clearly she's WW's favorite) is not conincidence.
Also, I'm not sure how much of the early game stuff is still relevant. Don't forget that, at this point, she barely knew the MC, he was just some guy that fit her criteras for pupils, and she could easily dose up with a lure.
After that, not only did he more of less kept contact with her, but she shared more than just a few "yo what I do now teach" scenes. You'd be fools to deny she very likely got closer/formed a closer connection with him that others. Sure she can be a bitch, but as the story progress, looking at it objectively, it's quite clear that he grew on her, and not only in a "you're my best guinea pig" type of way.
I'm honestly not so sure she'd be as ready to just throw him to his death as a lot of you seem to get at.
Actually, I think the more the story progresses, the more she gets attached to him and see him as more than a tool to use and dispose of afterwards. There are a lot of hints, a lot of moments where she's gentle compared to, for example, how she kept treating Jake like shit (not that he didn't deserve it), etc.
Ella is a very well written character.
Just as the MC is growing over time (not talking in power or size, I'm talking psychologicaly), she is also changing little by little. I doubt the current, end of version Ella would as easily flip out as the early game one would, after all that happened between those two points.