Ok, just in case anyone else would like to remove the retroarch setup screen from the emulation station front end, here is how I did it.
Exit emulation station by pressing F4.
Then CD /ect
CD emulationstation
Open es_sysytems.cfg with
sudo nano es_systems.cfg
Find this section and delete it:
<system>
<name>retropie</name>
<fullname>RetroPie</fullname>
<path>~/RetroPie/retropiemenu</path>
<extension>.rp .sh</extension>
<command>sudo /home/pi/RetroPie-Setup/retropie_packages.sh retropiemenu launch %ROM%</command>
<platform/>
<theme>retropie</theme>
</system>
Im sure you can just add # in front of each line to have Pi ignore it, if you dont feel safe about deleting it.
There is also a backup, es_systems.cfg.bak that you can restore from.
Then save, overwrite, and exit.
Then type exit to return to emulation station.
May have to reboot to see your changes, not sure.
The retropie setup screen should not be visible now.