It looks like Kodi uses ALSA on “dedicated” systems where it can safely control all audio, and “PulseAudio is used when Kodi is installed in a desktop-environment rather than a dedicated/direct boot setup. PulseAudio allows normal video & audio playback in XBMC while at the same time allowing the user to get audio in their browser or other applications.”
Do you still get the OSError: [Errno -9997] Invalid sample rate after you have PulseAudio running? If so you could try editing your asoundrc config file as described here: