You may not like the easiest way...
This behavior is defined in WiFi.h and WiFi.cpp. You could either modify WiFi.cpp to not write out wpa_supplicant.conf from WiFi.begin(ssid,pass), which will just use what is there or create a new begin() that takes no parameters and does the same thing. A new member function is less likely to break something else.
Reading the code is a beneficial exercise anyway. Dreadfully short on comments, but I guess we should be glad for any.
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As rmm200 said, as quick work around comment lines 252, 253, and 254 in the file <arduino-1.5.3>\hardware\arduino\x86\libraries\WiFi\WiFi.cpp, actually commenting line 254 should be enough but to be on the safe side the lines should look like this:
// sprintf(cmd, "wpa_passphrase %s %s > /etc/wpa_supplicant.conf",
// ssid, passphrase);