This is where I wholeheartedly disagree with you. That dead end that got interrupted by the 7th showed that the MC wasn't about to survive what was about to happen. I don't see how anyone can read that dialogue there and think he was about to come out alive. Especially when she straight up told the MC "she wanted to play with him a bit more" or that her telling him everything"wouldn't change his fate". That's not something you say to someone when you're taking them to an Apostle against their will.
I'm also not exactly sure why you're so sure Ella won't kill the MC when she has and will let him die on several occasions, even while knowing he has both traits. Unlike with Deryl, she hasn't given SIN or her students a no kill rule for MC. Hex and Cole tries to kill the MC once and Hex succeeded in dumping him in a monster realm in the 2nd. Aglaecwif straight up kills you if you say no to breeding. We also can't forget Ella herself kills you personally for killing Christie. You might say she was pissed but that shouldn't matter since she's so intelligent and wants a person with both traits, right? This is after Jake's final fight by the way. She didn't care about no dual traits and devoured him with her tentacles.
All of those events happened while Ella knows you have both traits so it's odd that you feel like she wouldn't off the MC for Jake, who she knows she can control and manipulate. Hell, for all we know, she only wants one Arbiter awake and not more than one.
You know what? I'll even level with you and say sure, she didn't kill the MC there in that dead end in her apartment. Sure, he somehow survived Ella's strike. That said, He definitely didn't survive beyond that scene and likely died when she got what she wanted. Which basically equals the same exact thing. MC was going to die no matter what. It doesn't matter if she didn't kill him there, he would've died later regardless because whatever she did was not good for the MC.
Now my question is; why DOES she kill us early on so much? SOMETHING happened after the end of our Training Arc. Ella has to be the most mix signaled and interesting person I've ever read. Let's break it down, I'll try not to be biased:
1. She apparently KNOWS us PRIOR to the beginning of the game; almost in an "obsessed?", close way.
2. We meet her and she gives us to the 3rd & 4th for powers. This is all for whatever plan she has?
3. Tells us to get stronger and sends various tests to kill us/strengthen us. If we die, we aren't worthy to carry into her plans to begin with, explaining sending Jake, Kenny, etc.
Dead End 4. Takes us to the 4th after we...progress too fast? It's in handcuffs but was it to actually kill us? Nothing good sure but death? I doubt it. We had only been doing EXACTLY what she wanted us to do just faster than anticipated sooo what gives? Regardless whatever it was, it was PART of her plans and up to the 4th. Remember; she DOESN'T work FOR the 4th or 3rd.
Dead End 5. We tell her about the Memory trait via the jellyfish move. This leads her to SHOCK and then murdering us. Why? We don't know. Perhaps because she thought SHE would be replaced as the 3rd & 4th's chosen??? Leading me to my next point...
6. She obtains Lvl 5, the 3rd (presumably) speaks to her and she says she ISN'T the one, whatever that means. Perhaps she thought she'd obtain the Memory trait after evolving? She does mention that Lvl 5s get "missions" "purposes" from their progenitors by that point if I'm not mistaken. Anywho, she mentions; must it be us? As if she had lost whatever major part of the plan she wanted to take the role of, leading yet again to my next point...
7. Our last Training Arc she comes off as...vulnerable? Almost defeated, as if she WANTS us to beat her and stop her plan (refer to Dracula, from Netflix Castlevania; she wants to die but has a drive to keep resisting until someone stops her?) Anyways her whole attitude of somberness pretty much stays with us, leading to my next point...
Dead End 8. She seems sad that we lose ourselves to the Arbiter. It's not a "I just lost my expendable piece of my puzzle" but more of a "close friend". Interesting consider the 'start' of our relationship?
Sidenotes:
A. She kills us for killing Christine, this was an impulsive act, we killed her best friend. She even seems pissed by the action.
B. She's collecting Monster hearts to combine them into the Arbiter's hearts and using them in some 'weird dark ritual'; Aglaecwif states.
C. At SOME point of time she finds out we have the dual trait but DOESN'T hunt us down for it like she does previously in the Jellyfish Dead End.
D. She knows BOTH our parents (refer to the pussy tentacle bedroom scene). If she doesn't have the Memory trait, and our Mom died during our youth, Dad is never around...HOW does she relate our parents to hers?
Sooo what gives? I'm getting mixed signals here. My guess is by the point of the end of the Training Arc, or even after we defeat Jake AND Deryl (Twice); we had already passed the threshold of irreplaceability. She does mention she's on a time table to get her plan done, so while Kenny failed to be a replacement at first, she does mention there were others she could turn to replace us because we were WEAK, but now we've already progressed TOO far AND she learned she wasn't "worthy" upon Lvl 5. It does make me wonder though, because Point 1. claims she actually was INVESTED in us on a personal level PRIOR to our original in-game meeting. So did we mean so little to her even with the personal connection? Did our worthiness later on make it personal more than her "interest" in us at the beginning? What gives? And before anyone says she's JUST crazy, she is; but when it comes to her plans she doesn't do ANYTHING without a reason. She's very calculative with every variable so much so she overthrew an entire Sector over the Week and managed to take on a bunch of Lvl 5s. Killing us for having the Memory trait initially wasn't an "I'm crazy Ella~" impulse moment.
don't you love the skill women have to make everything not her fault? Also don't call my dog fat 
