IMHO it would be a public relations suicide if they were still shipping new cars with bad transmissions. But who knows? It looks like the only way we'll know for sure is if new buyers don't post any issues in the next few months.
Maybe you need to consider it this way: If it DOES develop the problem, how will you feel and react? If you'll be satisfied with BMW repairing your new car, take delivery. If it will eat at you, make you really angry, etc. then maybe you should not take delivery.
Let us know what you decide. If you cancel, I'm certain a lot of people will be interested in what the dealer said, how you do/don't get your down payment back, etc. Good Luck.