I personally think that Ethan knew that Mia was a mercenary, or a bodyguard for higher. I think what she was lying about was that she was guarding "babysitting" a bioweapon. Mia also says during her initial fights with Ethan that he's been lying to her as well.
I also think there's absolutely no way it's a coincidence that Umbrella mysteriously waits three years until Ethan goes to the Baker plantation to also go there for "clean up". There are way too many coincidences in this narrative. I really hope Capcom doesn't wait until RE8 to expound upon Ethan and Mia's backstories.
Umbrella arrives due to Mia's codex pinging them when the D-Series specimens were acquired. Whether Umbrella wasn't the actual party on scene with Lucas (why would Lucas run from them if they were collaborating?) or Ethan acquiring these specimens signified an extreme shift in the situation that they needed to act on, that was the catalyst.
I love how nobody has an answer for this because no-one knows and it makes zero sense.
What doesn't make sense?
Zoe is infected and part of the family. She resists like Mia, but part of that may be due to her being a low priority to Eveline. Eveline is more concentrated on having a mommy and daddy than a sissy given her nature, a role that was already filled by Mia until Ethan could arrive so they could supplant Jack and Marguerite. This allows Zoe some bit of freedom.
Now, most of the story supports that Eveline wants Ethan to be Daddy [see next quote answer]. Being newly infected while unconscious likely, Ethan's cells hadn't been fully converted to regrow a limb, and having the hand sutured on would be less of a shock then the eventual regrowth.
Thus Zoe is allowed to reattach the hand as she assists in securing Ethan.
Now, the big question is why Zoe was allowed to or was able to get away with attaching Mia's codex to Ethan? Even if Eveline didn't understand fully what it was, she would know enough to not have that permitted.
Oh damn, at first I thought it was just a stupid game thing to not be able to shoot her, but it would make sense lore-wise, since she can control infected people.
Yet, Ethan is able to freely inject her while under overwhelming hallucinations.
Speaking of, here's a problem: why keep Ethan alive when at the point of Mia taking off his hand, Eveline wanted him dead (despite Eveline wanting him to be there in the first place?). Ethan didn't say anything against Eveline or had beeno offered into the family yet, so why have him killed?
The first time I viewed the ending it went past me since it's like ok, they are showing Evie was controlling Mia and this is what she was saying to her. Yet, additional playthrough show that it's quite disjointed from the rest of the game.
Everything done in the narrative with Eveline is terrible. Her character is all over the place in portrayal, the story beats don't add up, and the conclusion is underwhelming.