Using Lexi and Clark isn't really a good example. Especially since Danica one shots and kills the lvl 1 MC with her X during their fight. Not to mention, Clark oneshoting him in the sewer at Level 5. There's also a big difference between Ella encounter and with HERO earlier.
MC was high off of his instincts and his corruption increased dramatically during that first dead end. He was killing several people and had over 10 Corruption, which pushed his abilities further. Lexi was also a bad match up for regen types and Clark's attacks likely couldn't outpace the MC's healing(I'll have to recheck that dead end later). Not to mention, I don't even think the MC was conscious himself. He gave over himself to his power.
Now let's look at Ella's. Ella can possibly see the MC's core with her eyes, making instant kill extremely possible with only targeting his head and spine. MC only has around 13 power during that encounter and like 3 or less corruption, I believe. So it's not out of the realm of possibility that she could instantly kill him with all of that info. Also, your second reason actually supports her offing the MC. Because Jake having such high potential for Order, the supposed strongest power in game, means the MC, at that time, can be replaced or sacrificed.
We tend to forget that Ella doesn't really care all that much about the MC earlier on, even though the flashback later implies that she does care, she has no problem with him dying for her plan. That dead end at her apartment, when they fought, showed how she really felt and how she had no remorse for what's about to be done to him in the early parts of the game.
Well, corruption doesn't seem to affect combat ability in any observable way, and MC isn't that weaker during training with Ella, a couple of points at most.
Clark at level 4 lacks that huge pistol shot ability. He can only shoot small bullets. MC is a regenerator. If you wound him he can regenerate. If you completely annihilate him he can't come back. Alexis' attacks also seem to be small and localized as a level 4 and she unlocks the "huge sword" after reaching level 5, high in her post evolution trance and with help from Clark's empower ability. This plays perfectly into MC's abilities. In deadend17 Clark hits him with the huge shot and completely annihilates his upper half.
Danica can't oneshot MC with bodyshots. She can wound him badly, but he still survives. In all deadends during the double tag fight Danica cuts him in 4, MC groans, Danica gloats and then finishes him off.
Ella may be able to oneshot MC by crushing his head to smitherins so that's that. We have reason to believe that a small scale attack is still recoverable since level 1 MC can survive bullets to the head (scene in MC's house against Klaus, bullet implied to have penetrated the skull). Any other attack wouldn't work because Danica's attacks are both more powerful and cut off a huge part of MC's spine. Plus we know that MC can survive getting beheaded thanks to the scene in Klaus' prison cell. MC does not have other weak points other than his head and even as a level 1 he can easily survive small arms and similar attacks. Ella's favorite attack is using her hair throughout her level 4 career.
I agree that Ella doesn't give a shit about MC early on. The only reason he "survives" if they fight is because she learns of the double trait, leading to deadend3. As long as Ella thinks MC has only 1 trait, if he goes against her or against her wishes, she will kill him. However having Jake is NOT a reason to kill MC especially if she can't confirm Jake having the double trait. It is however a reason to manhandle him a bit harder, especially since she is already in a bad mood. Ella is one of the smartest people in the game, her knowledge is huge and her schemes meticulous. It makes absolutely zero sense for her to kill MC especially when we know that she wants a person with the double trait, and MC is the first to show it.
Edit: Actually replayed that part, she lets you live if you fight her with medium power. I thought she kills you.
