Well theres no real "Why" work is positive when done by the system. It's like how electrons are negative and protons are positive and current flows opposite to flow of electrons. It's just done by convention so we don't piss off Benjamin Franklin. You're free to make work negative when done by the system, just make sure you're able to keep everything straight in your mind, and make sure you're able to determine what the question is asking for. Odds are mcat questions will follow the general convention however.