I'm pretty sure it'll have to be all in one playthrough. Otherwise it'd be really easy. I had some problems with this one too. When you're getting the trains moving again in each section, don't get off to kill any guys; stay on the first car and blast as many guys as you can while the train is still going. After you've gotten all the trains running and if you still don't have the trophy, there are some guys on rooftops that you can kill while on the trains (this is easier if you haven't done many side missions though).