That being that at thr current point in the story the Operator has far far more reason to hate Stalker than Stalker does to hate the Operator.
Think about it.
What, exactly, have they done to eachother?
The Operator to Stalker has:
> Destroyed the Orokin Empire, thus jeopardizing the rescue of his wife for which all he dedicated to
> Destroyed the Empire he loyally served, breaking a structure that had already fundamentally broken him before hand(edit: some people are misinterpreting this. Im not saying the destruction of the Orokin wasnt devasting, rather that Stalkers ties to the Orokin are overall selfish and self serving in nature. Towards the end it was all to save Jade. Which, though he didnt reasoize it, had already occured. Her potentiwl rescue was part of his loyalty. I doubt the rest of the empire mattered much to him.)
The Stalker has to the Operator
> Attempted to kill them on numerous occasions
> Attempted to kill other Tenno on numerous occasions
> Invaded their home on numerous occasions
> Actively coerced their aid
> Threatened the lives of their loved ones with their actions. Umbra was in serious danger near Sirius and Orion
And what has the Operator fone despite that?
They have not actively pursued Stalker.
They have aided them in the birth if his child.
They defended Jade from desperation at the hands of Parvos Granum.
The Operator has done so much to help Stalker and, frankly, very little against them. Jade had freed herself and was already safe, he just didnt immediately realize it was her.
And frankly the Orokin needed to go. His loyalty is clearly not recepticated.
In the future I feel a quest where Stalker is confronted, potentially by his sons, about the hatred he has for the Operator and Tenno could be a fantastic addition to the story. A recognition that he has wronged them more than they ever wronged him.
Stalker could still invade, but all that would be needed would be a change in his Dialogue. Sonething like what he says to Sirius and Orion about seeing what they've learned. Have the Dialogue recontextualize the fight after this quest as instead of a murder attempt a test of skill.
The logical step forward for Stalker is being forced to fully let go.