Pontiac Vibe ECM recall

I have a 2006 Vibe purchased at about 30k miles. This summer we noticed some rough shifting when the car first started and kind of a ‘wind-up’ toy sound. We received the ‘recall’ in Sept2010 about the PCM, which mentioned ‘harsh shifting’ as one of the symptoms of a failed PCM. The letter mentioned possible dangerous conditions, so we decided to park the car, that our kids normally drive. The car was purchased for our teens. After waiting and calling the customer service number for Pontiac for three months, I finally got tired of waiting and took the car in to an authorized GMC dealer to see what was going on. To my suprise, and consternation they say the car needs a rebuilt transmission for $6500.00. My question is , could the PCM malfuntioning be responsible for the transmission failing at 57k miles? I was told ‘no’ by Mr. Goodwrench. The car has been with Mr. Goodwrench waiting for a response from the higher-ups at GM.