Cosmic rays interacting in the solar atmosphere produce showers that result in a flux of high-energy neutrinos from the Sun. These form an irreducible background to indirect solar WIMP co-annihilation searches, which look for heavy dark matter particles annihilating into final states containing neutrinos in the Solar core. This background will eventually create a sensitivity floor for indirect WIMP co-annihilation searches analogous to that imposed by low-energy solar neutrino interactions for direct dark matter detection experiments. We present a new calculation of the flux of solar atmospheric neutrinos with a detailed treatment of systematic uncertainties inherent in solar atmospheric shower evolution, and we use this to derive the sensitivity floor for indirect solar WIMP annihilation analyses. We find that the floor lies less than one order of magnitude beyond the present experimental limits on spin-dependent WIMP-proton cross sections for some mass points, and that the high-energy solar atmospheric neutrino flux may be observable with running and future neutrino telescopes.