Typing this before fully awake on my phone, so forgive the ramble, but I agree and would take it so far as saying the narrative was written depending on it:

I would wager that the department's rebellious attitude would have been dealt with much more firmly if it were not for Helly's presence and the events at the end of season 1 would never have happened. They were skeptical of everyone with Petey's incident, which they were forced to handle internally. Then Helly joined and it needed to go well. Who would be blamed for that PR stunt going wrong? Helly being hurt? Selvig, Milchick. The people that kept the issues secret.

MDR leaders wanted to protect their own image and kept hush about Helly's troubles. She threatened self harm multiple times, attempted self harm multiple times, tried delivering messages to her outtie, continuously broke rules.

Instead, Lumon made efforts to reward her and the team despite some major issues (Fraternizing with other departments, swearing at Milchick, fighting and biting Milchick, wandering halls after security doors installed etc etc) and goals not being met.

They wanted pictures of her and her team looking happy for the PR stunt and they were much more lax about punishment. They still punished, but again...lax...would be pretty bad looking if the Eagan keynote speaker showed up with fingers cut off because of their innie...or not show up at all because their innie had killed them.