We investigate the macroscopic behavior of the disordered harmonic chain of oscillators, through energy diffusion. The Hamiltonian dynamics of the system is perturbed by a degenerate conservative noise. After rescaling space and time diffusively, we prove that energy fluctuations in equilibrium evolve according to a linear heat equation. The diffusion coefficient is obtained from the non-gradient Varadhan's approach, and is equivalently defined through the Green-Kubo formula. Since the perturbation is very degenerate and the symmetric part of the generator does not have a spectral gap, the standard non-gradient method is reviewed under new perspectives.