It looks like its this part

while [[ -z "\$key" ]]; do
    \$es_bin "\$@"
    echo "EmulationStation will restart in 5 seconds. Press a key to exit back to console."
    IFS= read -s -t 5 -N 1 key </dev/tty

which is in
/home/pi/RetroPie-Setup/scriptmodules/supplementary/emulationstation.sh

Its the $es_bin that restarts ES, so I guess you could just take that out.
I really need to improve my scripting to understand it better though :)