To get rid of all of the Android partiion(s) you will first need to uninstall using the acme-uninstaller. Then if you run the Doctor, your device will be back to factory fresh state. I do suggest running the 'secure erase' option before the doctor just as a second level of protection to keep personal files from being pulled after an erase.
You seem to be contradicting yourself a bit. You do want to remove Android. Doctor will remove Android, but seems to leave remnants, from what I've heard. After all, it wasn't designed to detect and remove other operating systems.