I have no idea how to proceed. I had installed the gui as a last ditch effort because I couldn't nano into my klipper printer.cfg to edit it. I have since fixed my issue but now would like to remove the gui. Any help would be appreciated.
If it were me, I'd copy off my printer.cfg and start over with a fresh OctoPi image, then add the Klipper configuration back in.
Actually, if this truly were me, I'd have made a copy of my microSD before doing the PIXEL/Desktop upgrade so that I could easily fall back.
Use sudo raspi-config to change the startup option to not load the desktop.
I don't think that will keep the X window system from running. In theory, it will not run startx on the terminal.