I was also initially delighted with this new function, until it became annoying. I have not found a way to keep the phone from auto-playing via bluetooth, short of unpairing the phone from Sync altogether, thus losing the entire hands-free function of the iPhone in the car.
I did, however, find a much simpler way of stopping the music. I used to have to hit the home button and go into the iPod function of the phone and then press pause, since there is no actual "stop". Now I simply hit the pause button on the vehicle-side controls. Does the same thing.
I love the ver 3.0 enhancements, but this one needs a fix. Until a couple days ago, I was wondering what was eating my battery so quickly after installing the update.