Warthrop saying ''You are the one thing that keeps me human'', while feeling very satisfactory as a reader who has been frustrated by Warthrop's tendency to avoid any emotional conversation with Will Henry, is a truly horrifying thing to say to a thirteen-year-old child. To be fair, he didn't say it to Will's face, and given his reluctance to expand on it afterwards, it's clear it's not a sentiment he wished to ever share.
But the result is that Will Henry is now aware that he has a very clear role to perform for Warthrop and that if he strays from it, it will have grave consequences on Warthrop's character. Even though Will Henry often refers to Warthrop as someone cold and cruel - which is pretty fair considering the circumstances - it's also arguable that he might feel pride at the idea of working for someone who is very righteously principled: seeing Warthrop stands against murder, poor treatment, torture, etc, makes for a good example for Will Henry. And while Will Henry knows he's indispensable to Warthrop - and that it goes deeper than his apprenticeship - he didn't know until then that one of the indispensable services he provides for Warthrop is moral guidance/direction.
By hearing Warthrop saying that, Will Henry ends up shouldering the responsibility of keeping Warthrop human. He knows Warthrop can be good because he has seen it happen; he also knows what happens when Warthrop isn't and how people suffer for it (ex: the Stinnets situation). He would feel very keenly the weight of his burden, not only on a personal level - he wants Warthrop to be good - but also on a bigger scale - Warthrop's work has an impact on people (it saves people's lives on good days).
Will Henry's insane level of devotion to Warthrop in the Isle of Blood is tightly linked to his idea that he now has to keep Warthrop human. It's the first book where Will Henry makes plain that Warthrop needs him (usually, it's Warthrop who insists Will Henry is indispensable) and he also makes it clear that what Warthrop needs him for is something that goes beyond being his apprentice/assistant:
''He doesn't need me to cook or clean or take his dictation or care for his horse or any of that. Those things anyone can do, Dr. von Helrung. He needs me for the dark places.'' (The Isle of Blood, Chapter Thirteen)
Of course, it gives him a new sense of self-importance. He's the one who keeps the great Pellinore Warthrop human! It makes Warthrop's departure a hundred times more painful because it comes so soon after beind told how indispensable he was:
How dare he, after all we'd suffered together, after my saving his life more than once. You are the one thing that keeps me human. Yes, I suppose I am, Dr. Warthrop, until you find someone to keep you human in my place. (The Isle of Blood, Chapter Thirteen)
So there's a duality here. Will Henry is both crushed by this new responsibility, in the sense that he now has to protect something more fragile than Warthrop's life, and honored to be the one having to shoulder this burden. He resents it and relishes it at the same time. In any case, it's what drives him to action during the entirety of the Isle of Blood. He has to save Warthrop, both literally and metaphorically.
I had distrusted and then hated [Arkwright] for taking Warthrop from me, had tried and convicted him in my mind for a crime conceived only in my mind, and in the end it was not a ''bloody, soulless killer'' who had orchestrated his final test, no ''mean king'' as in Torrance's parable. No, it had been a thirteen-year-old boy consumed with jealousy and self-righteousness, casting himself in the role of protector and avenger of a man who had rejected him for another and exiled him from the rarified atmosphere of his presence. (The Isle of Blood, Chapter Twenty-Six)
Will Henry goes far to serve Warthrop; he goes even further to protect him. In book 2, when he kills Chanler, it's framed as an act of self-defense and an act of protection. It's the morality of the moment, Kearns would say: Will Henry has to kill Chanler to make sure both he and Warthrop survive the night. Afterwards, this death is treated as something that was necessary and therefore forgivable (but not forgettable). In addition, it's less about killing Chanler and more about killing a soulless monster. It's less a moral dilemma and more an emotional conflict (killing his master's best friend).
When Warthrop says, ''You are the one thing that keeps me human'', it implies that Will Henry is able to do so because 1) Warthrop cares about Will Henry's opinion and will adapt his choices to Will Henry's approval and 2) Will Henry is a child who represents innocence (re: the motif of the bucket). Innocence is associated with goodness and purity: Will Henry is the one person whose judgment carries weight for Warthrop because, to the monstrumologist, he is the epitome of a possible absolution.
But Will Henry loses that. He is no longer innocent:
''They may be a different color, but we've the same eyes, Master William Henry, you and I. Occulus Dei - the eyes that are not afraid to look, that see where others are blind. [...] Your eyes have come open, haven't they? It's why he keeps you with him, because you see in the dark places where he is afraid to look.'' (The Isle of Blood, Chapter Forty-One)
If I confessed, there would be no absolution; I would still be nasu. (The Isle of Blood, Chapter Thirty-Three)
And he is no longer good (in the sense that he starts considering immoral actions to solve problems):
I looked past him, to the sea framed in the arched opening of the wall, to the line formed where the water met the sky. The world was not round, I realized. The world was a plate. (The Isle of Blood, Chapter Thirty-Two)
Everything that made Will Henry morally capable of steering Warthrop towards the light is gone. Paradoxically, it is only by losing these qualities that he can protect Warthrop's own sense of moral. By taking it upon himself to cross the invisible line and kill, he protects Warthrop. If he were to reveal his misdeeds to Warthrop, he would drag him down too:
He would be made unclean by my touch. My ''success'' at the Tower of Silence would be his failure, the fulfillement of his deepest fears. He would know beyond all doubt that by my saving him he had lost me forever. (The Isle of Blood, Chapter Thirty-Three)
This is what has to be given to fulfill his role as Warthrop's indispensable apprentice. This is what Will Henry has to do to keep Warthrop human. He cannot even obtain the absolution of confession because confessing would not save Warthrop. Will Henry lies by omission - lying is the worst kind of buffoonery - because this is what he feels he must do, what he has internalized from Warthrop's ''You are the one thing that keeps me human.''
In essence, The Isle of Blood is Will Henry's desperate attempt to save the humanity in Warthrop. Ironically, Warthrop is doing the same thing:
''The very strange and ironic thing is that I left you behind so you wouldn't have to live on that plate with them. (The Isle of Blood, Chapter Twenty-Six)
Both fail. But where Will Henry's failure rewards him - it gives Warthrop a new sense of urgency to do anything he can to protect him (the ''I will raise you upon my shoulders'' scene) - Warthrop's constant failure is what cements Will Henry's loss of innocence. Where Will Henry manages to keep Warthrop human (his love for the boy takes precedence over Will Henry's potential to effectively offer absolution), Warthrop fails to keep Will Henry from crossing the line between a round world and the plate-world.
In the end, ''You are the one thing that keeps me human'', while a touching sentiment and a proof of Warthrop deeply caring for Will Henry, is still the egotistical product of what he calls the dark tide. It sweeps Will Henry in a darker world, one where he feels he has to give himself up so that Warthrop can live in the light:
I had failed him and I had saved him. I had gone down to the darkness that he might live in the light. (The Isle of Blood, Chapter Forty-Two)
Will Henry may not have been born with the mark of Cain on his forehead, but ''You are the one thing that keeps me human'' left a much deeper mark on him.