Hmm, I have some counterpoints.
1) Nyx mentioned that MC took it like a champ. It seems that his resistance to pain was unusual. Ella was also in the middle of doing something. Falling on her knees could easily be due to her losing concentration. There is actually nothing saying that Ella can't feel paralyzing pain. Level 1 MC's poison was enough to make her squirm during deadend3. Yes she was level 4 at the time, but still the power difference was huge.
2) I don't have any reason to believe that Ella is "struck" by something. That red miasma is her own expression of power. She starts summoning her power, threatens to kill them, but mid sentence she drops to her knees and loses her concentration. We've seen her do it numerous times, like when she evolves, when she transforms into that goat thing etc. There is no external agent causing that red miasma. It's all Ella.
3) MC wasn't struck by energy when he received the mark. Only the tattoo was green initially and there is no reason to assume it would glow through clothing. All Nyx has to do is raise her hand. Malik and Nico could completely miss it if she wanted to hide it but personally I doubt that she even tried to hide it. The only problem I find here is that Nyx wanted MC to strip so it may require a visual component, but it could also be for her own entertainment.
4) Nyx has claimed in the past that she likes to mark humans before killing them to gain more corruption. She is known to do this. Additionally Ella is a possible resource for HERO and even in the latest update Xanthe is still bitter for not getting info out of her. Ella and Nyx working together could still be true, but this explanation doesn't require it and perhaps Ella may even manage to convince Nyx to revive her.
5) Deus knows that Ella will survive anyway. He tells MC to not face her, keep his secrets close and don't tell her shit unless he is strong enough to impress, because her eyes see much but she doesn't have the correct understanding. MC is nowhere near strong enough to impress. This pretty much confirms that he believes Ella will come back and in full force. The only question is what Zack is going to do about it. He probably knows it too, and if Nyx killed her, it doesn't take a diviner to figure out who did it, especially if the body they have in captivity vanishes.