The problem is a disconnect in threat models.
An attacker with physical access can defeat any obfuscation scheme that doesn't require input from the user.
The point of having a wireless key stored in plaintext (or obfuscated) is so that the computer can connect to that network without input from the user.
Encrypting the key requires input from the user, so storing the key is effectively pointless. Obfuscating the key doesn't actually do anything to stop anyone with root access. Whatever choice you make you will break either the security or the usability.
Why break the security? Because the security is minor, in this case. An attacker with physical access to a computer on the site of the wireless network can already compromise the wireless key, eg by using a keylogger, installing malware on the machine to sniff the wireless key from memory as the computer initially connects, and possibly reset the access point's settings, assign a new key, and assign a new key on the client computer (s). etc. An attacker with physical access to a computer off the site of the wireless network (coffee shop, etc) just stole your computer, and is probably going to sell it. If they're determined to attack your network the same issues as above arise.
So not storing the key requires the user to type it (or a password to decrypt a keyring) when they connect, and provides very little practical security benefit. Anyone who would derive a practical security benefit from encrypting the key would likely derive a much greater security benefit from using a wired connection. The benefits are outweighed by the costs.