We study level-set percolation for the harmonic crystal on $\mathbb{Z}^d$, $d \geq 3$, with uniformly elliptic random conductances. We prove that this model undergoes a non-trivial phase transition at a critical level that is almost surely constant under the environment measure. Moreover, we study the disconnection event that the level-set of this field below a level $α$ disconnects the discrete blow-up of a compact set $A \subseteq \mathbb{R}^d$ from the boundary of an enclosing box. We obtain quenched asymptotic upper and lower bounds on its probability in terms of the homogenized capacity of $A$, utilizing results from Neukamm, Schäffner and Schlömerkemper, see arXiv:1606.06533. Furthermore, we give upper bounds on the probability that a local average of the field deviates from some profile function depending on $A$, when disconnection occurs. The upper and lower bounds concerning disconnection that we derive are plausibly matching at leading order. In this case, this work shows that conditioning on disconnection leads to an entropic push-down of the field. The results in this article generalize the findings of arXiv:1802.02518 and arXiv:1808.09947 by the authors which treat the case of constant conductances. Our proofs involve novel "solidification estimates" for random walks, which are similar in nature to the corresponding estimates for Brownian motion derived by Sznitman and the second author in arXiv:1706.07229.