Spin ice presents a typical example of classical spin liquid, where conserved magnetic fluxes emerge from microscopic spin degrees of freedom. In this letter, we investigate the effect of perturbation by magnetic charge disorder in two-dimensional spin ice. To this aim, we develop a novel cluster update algorithm, which enables fast relaxation of magnetic charges. The efficient Monte Carlo calculation reveals a drastic change of spin structure factor as doping magnetic charges: the pinch point, characterizing the spin ice, is gradually replaced by a diffusive peak. We derive an analytical relation connecting the flux fluctuation and the spin structure factor, and explain the evolution of diffusive peak in terms of the roughening of magnetic fluxes.