I agree. If they're paying you to do something, you basically do it, or you don't get paid. You don't own the code, the company you're contracting for does -- if they want it a certain way, you're pretty much obligated to make it that way. If the boss wants code that has every line documented, and you refuse, I can bet he won't be keeping you around for too long (as unfortunate as this particular situation is).
scott.