I don’t think I’ve seen this said before, but it makes the most sense of anything.
John left Gideon mostly dead and with visible indications of this (the speed holes) on purpose specifically to stop Harrow (and others) from killing him. This is kind of his thing. He’s miserable. He wants people to like and to understand him, but he doesn’t know how to make people listen to or like him anymore without holding hostages. He’s holding all of the nine houses hostage too. But he’s realized they can leave if they really do want to because the entire sixth house did just that. And he can’t force every member of the nine houses to be directly dependent on him by using his power to somewhat consciously keep them alive (at least not any more than he already does). But he can do that to Gideon. And Gideon is important to Harrow, and Harrow is important to the entire ninth house and to the warden of the sixth and to Pyrrha (because of Nona) and Ianthe. And if Gideon actually dies, he doesn’t know what Harrow or anyone connected to her will do and neither does Harrow. The girl already did her own brain surgery because she thought it would stop Gideon from dying. So Gideon is now an insurance policy. Something tells me this will be important very quickly in Alecto.