I'm not sure. Is ponyprog a software, or the hardware? The stk200 is the software, right? You might be able to use avrdude by creating a new menu item in the Arduino Burn Bootloader menu. Just edit the ARDUINO/hardware/programmers.txt and add something like:
stk200.name=STK200
stk200.communication=usb
stk200.protocol=stk200
The communication preference should be serial if the stk200 uses a COM port (either a physical serial port or a virtual usb-to-serial COM port) or usb if it communicates directly as a USB device. Or parallel if it uses the parallel port.