We study the self-energy of phonons, magnetoelastically coupled to the two-dimensional Kitaev spin-model on the honeycomb lattice. Fractionalization of magnetic moments into mobile Majorana matter and a static Z2 gauge field lead to a continuum of relaxation processes comprising two channels. Thermal flux excitations, which act as an emergent disorder, strongly affect the phonon renormalization. Above the flux proliferation temperature, the dispersion of a narrow quasiparticle-hole channel is suppressed in favor of broad and only weakly momentum dependent features, covering large spectral ranges. Our analysis is based on complementary calculations in the low-temperature homogeneous gauge and a mean-field treatment of thermal gauge fluctuations, valid at intermediate and high temperatures.