I figured it out. The command I used is:
sudo security delete-generic-password -l $ssid "/Library/Keychains/System.keychain"
sudo was needed because this keychain is located in the systems library. security
also contains a lot more delete and useful commands and you can specify how you want to indicate the location in this command.
edit: I was having some trouble using this command and went back and learned I could use another command to not remember the network at all which I would have used before if I had found it. With this option you can do a wealth of things with your adapter along with the networksetup option.
Here is my final script which first runs as root. then it changes the system preferences to not remember new networks. Then it disconnects from any current networks. Then it adds the new network. Lastly, it makes the system remember new wifi networks.
sudo -i
sudo /System/Library/PrivateFrameworks/Apple80211.framework/Versions/Current/Resources/airport prefs RememberRecentNetworks=NO
sudo /System/Library/PrivateFrameworks/Apple80211.framework/Versions/Current/Resources/airport -Z
networksetup -setairportnetwork en1 $ssid $password
sudo /System/Library/PrivateFrameworks/Apple80211.framework/Versions/Current/Resources/airport prefs RememberRecentNetworks=YES