I'm getting tonked on Top Player but I'm still not conceding many, if any goals from through balls, especially compared to PES2012. My main tactic, which others have said, is to use the right stick to take control of your last man and use him to backpedal and keep track of the striker. I often do this and the AI simply decides it doesn't fancy the through-pass after all.
I've done this so much now that I've started getting risky, keeping pace with the striker's run then trying to time when the CPU will play the pass (when it does decide it wants to try the through-ball) before making my man I'm controlling move in the opposite direction in an attempt to catch the striker offside. It's risky but I've gotten quite effective at it