I think I got it. It appears android keeps this config in memory. It actually doesn't restore it during reboot. It restores it AFTER you've edited the file. To get the files committed for good you need to:
1) Turn off your phone's WiFi
2) Mount /system in rw mode and then rename or delete /system/etc/wifi/default_ap.conf (this file restores the data in the wpa_supplicant.conf). This is where your phone sets/copies the wifi you can't get rid of.
3) Edit the /data/misc/wifi/wpa_supplicant.conf file. (I'm guessing deleting it would be a bad idea since there's no backup data in memory to generate this.)
4) Save the file.
I have an SGS5 SM-G900K. Had to do some cleaning due to some bloatware and some wifi configs I don't need. It might work for you.