The $W$-random graphs provide a flexible framework for modeling large random networks. Using the Large Deviation Principle (LDP) for $W$-random graphs from [9], we prove the LDP for the corresponding class of random symmetric Hilbert-Schmidt integral operators. Our main result describes how the eigenvalues and the eigenspaces of the integral operator are affected by the large deviations in the underlying random graphon. To prove the LDP, we demonstrate continuous dependence of the spectral measures associated with integral operators on the underlying graphons and use the Contraction Principle. To illustrate our results, we obtain leading order asymptotics of the eigenvalues of the integral operators corresponding to certain random graph sequences. These examples suggest several representative scenarios of how the eigenvalues and the eigenspaces of the integral operators are affected by large deviations. Potential implications of these observations for bifurcation analysis of Dynamical Systems and Graph Signal Processing are indicated.