We present a microscopic open quantum systems theory of thermally-damped vortex motion in oblate atomic superfluids that includes previously neglected energy-damping interactions between superfluid and thermal atoms. This mechanism couples strongly to vortex core motion and causes dissipation of vortex energy due to mutual friction, as well as Brownian motion of vortices due to thermal fluctuations. We derive an analytic expression for the dimensionless mutual friction coefficient that gives excellent quantitative agreement with experimentally measured values, without any fitted parameters. Our work closes an existing two orders of magnitude gap between dissipation theory and experiments, previously bridged by fitted parameters, and provides a microscopic origin for the mutual friction and diffusion of quantized vortices in two-dimensional atomic superfluids.