It will work. The Arduino board is just the Atmega328 plus various peripherals for easier connectivity to computer, voltage regulation, etc.
But instead of doing it on protoshield/stripboard, I suggest you just make a breadboard Arduino first (only requires about 5-6 parts), test it out with the Ethernet shield, then move your circuit to the stripboard.
Here is breadboard Arduino: http://arduino.cc/en/Tutorial/ArduinoToBreadboard