Figured it out. Typing
killall wpa_supplicant
fixes the issue (solution found at http://azitech.wordpress.com/2010/02/22/deauthenticating-reason3/). Turns out I didn’t need to set the channel first, but in order to do so I found I had to specify an essid first before it would accept a set channel command.
Anyone know how to just disable wpa_supplicant from starting in the first place? systemctl disable didn’t do it. Right now I have a separate service script run at boot just to kill wpa_supplicant.