Thank you for acknowledging that Stella isn't innocent however there are points in your argument that I want to address.
Points 1 and 2: Yes, we don't know who came up with the idea. We do know when it was implemented.
And the book says "orphans are no longer permitted to bring toys made by other companies" so this is something that got implemented around the publication of this edition of the notebook. It also says that "if employees see toys from other brands while working here, they are to remove them".
In the orientation notebook there's a poster advertising Boogie Bot that says "Coming Soon in December of 1993" indicating that the book takes place in 1993.
So maybe it wasn't Stella's idea. But Stella is in charge of Playcare where it was enforced. Stella is the one who the counselors who enforced this rule answer to and may have enforced it herself.
It's like how Harley Sawyer is still responsible for experimenting on the orphans, even though the ARG points to Leith being the one who came up with experimenting on orphans and offering them to Harley to begin with. Of course, it doesn't matter to me whose idea all this horrible stuff was! Sawyer chose to experiment on the orphans and Stella chose to implement the rule.
Also PW's note indicates that this rule was implemented quite strictly. Since his note about the policy he only adds "...And the kids are not allowed to ask what happened to their old toys [...]". Not only does this sound like behavior of a loosely implemented policy, but if it weren't as harsh as it sounded it seems like something he would comment on.
I've developed a fawn response and escapism tendencies myself which I believe are due to childhood experiences, so I understand what you're trying to say. Because while yes, directly saying "No" to Leith would have gotten her killed almost certainly, she had so much time to do something behind his back. To report it. She had many opportunities to leak the documents to someone and figure out who would be safest to tell. She's been part of the experiments since January 1991, possibly even earlier.
There is a theory she was the one whose omni hand was used to kick off The Hour of Joy, and maybe she's just very scared, I used to think before Chapter 4 The Schoolhouse's new curriculum was just something Leith ordered Stella to write, but honestly Chapter 4 really has completely made me do a 180 on her. The way she says, "I see." when Leith tells her they're still "working out a timeline". The way the caption "Stella makes her decision" which doesn't really sound like she's just saying what Leith wants to hear.
Leith is very clearly abusive towards Stella, I picked up on that as well. However, the moment you are referring to ("We did what was necessary, Ms Greyber") is in the aftermath of the theater incident. However, I don't think that that one exchange is entirely indicative of Stella's role in Playtime Co. Yes, Leith talks over her and intimidates her when she speaks in a way he doesn't like. But she's not completely powerless.
The tape where Stella talks about boundaries is in "The Doctor" VHS. Leith actually cuts her off only once to say "I'm not disagreeing". I mean he is lowkey disrespectful to her, but she does get to speak up without being punished.
Actually the tape where Leith cuts Stella off in the aftermath of the theater incident, not "The Doctor" VHS where Stella talks about her boundaries at all.
The tape where Stella talks about her Playcare boundaries (The Doctor VHS) she actually is much more outspoken and talkative towards Leith. When Leith firmly tells Eddie they can't kill Sawyer Stella (quite loudly and with a great deal of conviction) declares, "Eddie's right though - Sawyer can't keep leading this project!" And Leith initially acts dismissive, he quickly placates her by adding "I'm not disagreeing". So yes, Leith does talk over her and verbally abuse her on occasion. But this isn't their entire dynamic. Stella is one of the four holders of the omni-hand in the factory. She has power.
I'm glad that you recognize this, I just feel like it's really important we don't dismiss what power she does have.