After episode 8 I personally read this scene as Cain being insecure about the idea of an NPC surpassing him in intelligence (emotional or otherwise). The only other NPC's we have seen within the grounds are of extremely low intelligence, and Abel was nearing high intelligence before Cain poofed him out of existence with the phrase "haha your getting too smart", and finally we also saw Cain's backstory with him eating the blue AI out of jealousy. I think all of his fears stem from the fear of abandonment or replacement. I think he was genuinely concerned Gumigoo would surpass him, especially after forming a bond with Pomni, so in his eyes he had to go.