"Good. Kill him and let's go." He drops Scorpius back, onto the table, and Scorpius opens eyes and mouth wide. "What?" John shrugs at Aeryn: "Kill him and let's go." Aeryn gapes at him. "We came here to free him." No, John clarifies: "We came here to make sure that my knowledge didn't slip out of his mouth. Kill him, Aeryn, and let's go." She considers him: "Oh, you want me to kill him?" And John's like, "I'm not the assassin here." She shakes her head, unhappy with all this. "If you want him to die, you can kill him yourself." John says she made him promise otherwise, and on his request she releases him from that promise twice. He thanks her, and pulls Winona on Scorpius's face. And waits. And stands, with the gun pointing down.
So this is happening on like six levels simultaneously. Let's work backwards. Aeryn's vow of protection, for Scorpius; John's corresponding vow; Scorpius's protection of John. Aeryn and John's unquestionable concern for each other. It's a triangle of mutually assured protection but also taint, and Aeryn brought that into their bed, and she did this thing wearing a coldsuit, and bearing secrets and mysterious babies. It's no coincidence that John brought up her assassination history: he's not talking about Velorek, he's talking about Harvey's Lovely Daughter. She releases him from this vow, this darkness she's introduced into his relationship, as she waves away the last of the secrets that stand between them. We know, although John still doesn't (although he um totally does), that she's only ever loved John. That the dark time is her propaganda and the ghost of her fear, and that she's tired of its weight. Getting bored with it. She's done the work necessary to enter into this relationship naked, no secrets and no armor, and so has he. No more Scorpius, no more Harvey, no more coy dancing around the baby, the physical and vulgar truths about it all. He can beg her for permission to shoot Scorpius in the head, and she'll give it again and again, but the universe laughs at him for asking her to do it herself. She already did. And while she was doing it? He was basically sleeping with Scorpius. Letting him in far enough that he earned himself a Harvey; a Harvey that asks, as he always does, to put Scorpius before Aeryn herself. Shoot him for you? No. As long as we didn't know who the father was, as long as we didn't know what Aeryn was up to, that baby was just Harvey in another form. She gave everything she had, and more, for that baby. Be a man.