What are the alignment specs after it was done? Is the car lowered? Lots of negative camber?
Although some people like to run a bit of toe in on the rear for better hook up, or run a bit of toe out for less understeer, anything but dead straight will affect your high speed stability especially in rain or snow.
I am positive that your subframe is not damaged. That issue would manifest itself in many different ways before affecting your alignment.
Your car is 2004 and subframe damage is very rare in vehicles made after 2002.