The mind control Ni uses on those she resurrects only fucks with how they perceive the world in order to align them with
her goals. It's not out-and-out puppeteering.
From Sega's point of view when she was under the effects of the Control Seal, she believed that the Unified Darkness were the good guys, and that Nepgear was just a bit misguided and/or being controlled against her will. So, being Sega and an over-protective big sister, jumped through the closest portal to run her down and drag her 'back'. Similar stuff is currently happening with the available girls.
They've all had their point of view twisted to see following Red as their desired path. For most, this is rather straight forward by simply switching who they see has the good guys and bad guys, but for others it leaves huge holes that can lead to them Blue/Orange-ing themselves out from under her control.
Like Sega.
Or the mind-fucked mess that White Soul is.
I'll probably be going into White Soul's motivations during her fight.
I think I remember someone saying that oblivion awaits at full strength is a world killer, and grey can very easily produce buff someone way past that level of fire power if they are even slightly dangerous. I mean it's not like the demons would flinch at killing humanity.
Oblivion Awaits can cause destruction on continental scale. As in, it can turn North America into a flatland.
And while it's true that Grey Champion could boost certain people to the point of being able to pop a planet, they still have enough free will to decide to do it or say "Hell NO."
And true, while the Demons in command wouldn't flinch at killing an entire species off, Grey Champion still has enough of a "Hero" mentality to balk at it.
The nature of Goddess Red's mind control and how it interacts with people that share Grey Champion and Goddess Grey's mentalities will actually be a significant plot point some time after you guys rescue Ichi.