Both of those dead ends were before the MC evolved to level 2. For me, I'm of the opinion she found out about his Memory Trait when he reached level 2. Around the time before he really fought Jake. The reason for that is because he started using it a lot around that time and because Deryl was on Ella side since the beach. He also likely had Zara's mark with Charlie's oath and told her everything about the MC.
As for the helping part, I've pretty much said the same, with Deus. His "help" just amounts to allowing her plan to succeed.
The serums aren't for Ella. They're for the people she has on her side that are stuck. The dangerous superhumans, monsters and so on are worth the effort. Especially because they'll likely join her side and fulfill her needs. It's not about Klaus or the others bodies. They're completely irrelevant actually and have no benefit. She won't be summoning the Apostles anytime soon so it's not an either or choice and it's not like this action wouldn't contribute to the act itself.
She likely did struggle to get 8 hearts, especially since she complained about the purity of them. So why take the extra time to gather more of the perfect purity when you can just get the "uncategorized" bodies from HERO that have guaranteed purity? Her body is also not contained in the power nullification room. As far as I know, the Negative Energy is still flowing through her. Malik and the others are confident that she's dead so they likely don't have her in that room. If they did, they wouldn't have to wait until it wore off to dissect her.
Ella stands to gain a lot from this infiltration. Serums, monster gear, information on HERO's superhumans, possible Apostle corpses and the locations of others that were found by Deus and Zack over the years. Then there's the new imprisoned allies and the MC. That's all worth it. Especially since she didn't lose a damn thing during HERO's infiltration of her base, like I pointed out. None of her students really did anything besides standing around. Hex, Goliath and Aglaecwif all got away so nothing of value was lost.
Why would Ella play around and not escape if it wasn't intentional? If her failure was set in stone from the start and she knew it, why would she willingly do the dumb thing and make herself large enough to be hit by Nyx? She already knew about Nyx's power. Why didn't she escape after ordering the others that they're retreating? She was still busy fighting with Nico. Unless you think her ultimate goal was to kill Nico so she can trap Malik and them in the collapsing dimension but she would've known that would fail as soon as he broke free so why would she continue to stall?
Using your own thought about Aglaecwif against you, why didn't Ella leave after she got bred then? If getting her loyalty was one of the goals then she completed that earlier on. In fact, she completed all of her assumed goals, minus killing Nico, so why was she still there? Why didn't Hex teleport her away? We know he can do it, even if Nico is there because he escaped with Cole and them during their fight.
So for me, I'm thinking her goal was always to use her own body as a trojan horse to get back into HERO. She intentionally got herself hit by Nyx. All so she can gather resources and beings for her own side, outside of SIN. I don't see my stance changing on this until we get further info.
