Lexi told Clark that Deus is back. As they went inside, Malik tells them Deus went out but he should be back soon. Guess what happened when he actually got back? He let the MC come in by pressing the elevator and directly talking to him before telling him he should leave before getting swept up in the infiltration. That's actually helping someone do something they shouldn't be doing and fully being an accomplice.
I also think your misunderstanding something about Deus with your "his organization" comment. A lot of you forget that Deus is on his own time, figuratively and literally. He's not loyal to anyone but the future. MC is a very important part so he'll help him along. Ella plays a part in the MC's future so he won't halt her plan. That doesn't mean he's actively helping her succeed like he does with the MC. That just means he's going let her do whatever she wants up until whatever plan she has comes to completion.
I'm aware he's not really loyal to anyone, though his objective still alludes me.
So it would be safe to say, like the MC asked; he WOULD not capture her until she's finished her work? Therefore wouldn't he
technically be helping her albeit indirectly in some cases if say:
A. He let her break into their facility and Evolve to Level 5.
B. Chose to "sit out" (night terrors) when H.E.R.O was discussing what they knew about Ella.
C. H.E.R.O thought they killed her and he failed to mention the information that she still poses a threat in the foreseeable future?
D. Knowing what her plan is yet not telling anyone who may try and stop it?
I dunno, if someone did allll that for me I would consider that
help, despite whatever underlining intentions their end goal actually is. At the very least, right now, he HAS helped her, though he's also went against her at the same time obviously. They are technically "enemies" but as of right now I'd say they are distanced "frienemies" till she completes whatever task Deus needs done.
On an unrelated side notes:
Deus said that there were going to be simultaneous attacks around the Sectors. I can't remember if they elaborated further but did that ACTUALLY happen? I'm assuming it did given Bernhardt's travel speed but if it didn't perhaps that was to prolong the main fight so that we could Evolve properly against Deryl.
I also find it funny that anyone in their right mind would trust Deus. Given his ability he'd be able to live or even beat however or whomever he wanted, so the fact that he CHOSE to come to H.E.R.O willingly especially given how shifty he is would set off my red flags. Zack makes sense cause he helped WAYYY back originally and you can see where his loyalties lie, but Deus...they don't really know Deus. The only one I've seen wary of him is Dexter, but Malik and the rest of the Lucifer squad practically love him.