I don't actually remember Jin-woo saying he will devour the system in the novel. It just says that the system turned its back on the Architect (creator of the system). I just assume that the system needed Jin-woo so it wasn't willing to discard all those efforts. Also, the original Shadow Monarch did choose him like the Architect said he was "against choosing Jin-woo." And the System was made to make Jin-woo stronger so that the original Shadow Monarch could descend and take over his body. That's why Jin-woo wasn't supposed to keep his ego, but the original Shadow Monarch took a liking to him