gone completely
Remove package retropiemenuunder "core packages" in the retropie-setup utility.
Remove directory ~/.emulationstation/gamelists/retropie and everything in it.
Remove directory ~/RetroPie/retropiemenu and everything in it.
Edit /etc/emulationstation/es_systems.cfg and remove the "RetroPie" system entry:
<system>
<name>retropie</name>
<fullname>RetroPie</fullname>
<path>/home/pi/RetroPie/retropiemenu</path>
<extension>.rp .sh</extension>
<command>sudo /home/pi/RetroPie-Setup/retropie_packages.sh retropiemenu launch %ROM% </dev/tty >/dev/tty</command>
<platform/>
<theme>retropie</theme>
</system>
If you have one at ~/.emulationstation/es_systems.cfg, make the same edit there.
I think that should about cover it? Now...
hoykey for retroarch
Edit your autoconfig file for your gamepad(s) at /opt/retropie/configs/all/retroarch/autoconfig/[gamepad device ID].cfg and remove all lines that look like these (your values will differ, and it may say axis where this says btn or vice-versa):
input_menu_toggle_btn = "3"
input_reset_btn = "0"
input_save_state_btn = "5"
input_load_state_btn = "4"
input_state_slot_decrease_axis = "-0"
input_state_slot_increase_axis = "+0"
(Probably leave "enable_hotkey" and "exit_emulator" intact, or your players won't be able to quit, or will quit every time they hit Start.)