EL wire and Raspi- is it safe and possible?
You're on the right track in that you need to control the EL wire at the power supply input (equivalent to popping the batteries in/out, or activating its mechanical switch). You definitely don't want to try switching the output side; the output is ~100V AC which is harder to deal with.
Here's something to get you started:
You can model your EL wire power supply as a load that needs about 3V and something less than 1A. (Based on the ~6 hour life I've observed from them, it probably draws around 100-200mA, but it's better to design for 1A to be conservative.)
Raspberry Pi GPIO pins are limited to about 20mA output, so you'll break your Pi if you try to make a GPIO pin power the thing directly. Instead, you need to make the GPIO pin control a transistor (an NPN or NMOS rated for 1A or more) which will handle the switching of actual current.
So your circuit should be:

GPIO -&gt; 200 ohm resistor -&gt; NPN transistor gate
Power supply battery compartment (-) -&gt; NPN transistor collector (the higher voltage side)
Actual battery (-) -&gt; NPN transistor emitter (the lower voltage side)
Connect a wire from actual battery (-) to the Raspberry Pi GND. (This will be the return path for the current sent into the transistor gate.)

If you look up circuits to control a motor from a Raspberry Pi, it's the same idea. Basically the NPN transistor switches the low side of the load, so when it's on it will connect the EL power supply (-) to the (-) of the battery. You can use the same transistors and resistors that people use to control motors.