You are using mupen64plus-libretro with rice plugin at the moment. Use another emu or plugin. Press x/m at game startup and select another one. MK64 + RetroPie Beta 2 runs fine with:
mupen64plus-libretro + gles2n64 plugin
mupen64plus + rice plugin
mupen64plus + gles2n64 plugin
mupen64plus-testing + rice plugin
mupen64plus-testing + gles2n64 plugin
Mupen64plus-libretro + rice is default because it does not crash your pi with certain games and uses retroarch controller setup. Mupen64plus standalone should be faster but needs more effort to setup unknown controllers and hotkeys.
yes, you can make mupen64plus gles2n64 (testing) the default, and it should be, not only for that ROM, but for N64. The only exception I have really found is Zelda, which runs better with Rice. Mario Kart runs sweet with the (testing) mupen64plus.