[@KoL]
Might not be my place to speak, but I'll throw in my 2 cents anyway.

It appears to me as if the factory was evacuated by lmpkio's guys for good reason. They were in a situation they could not win, threatened by two beings that could not be defeated by any means available to them. As such their options were either to evacuate or to die for no real reason.

While I'm not arguing that they should not be punished for contradicting orders, I am arguing that lenience should be given due to the particular circumstances.

Assuming that whatever 'Harley' leaked to Eos about their research doesn't get Eos to murder them all anyway.

Regarding Lilian, she evacuated an exploding facility in order to not die. Now she's looking over the battlefield to see whether she's needed, and where she might be needed. It seems to me that Lilian has not yet contradicted Eos' orders.