You might not remember, but BT had a nice crack in his case and was able to use JB Weld to repair it and it is still holding.
Before 
After 
IIRC, he used 99.9% Isopropyl Alcohol (basically pure rubbing alcohol) to clean the area before applying the Weld.
Ideally, you would probably want to crack open the case and put something behind the hole when applying the weld. That way the inside portion of the weld would be smooth. But I know that is probably not going to be the easiest way to do it.
Also, if it punched a hole 3 inches wide, then I would be scared of what was inside the case either way. So... pulling it and taking the case apart might not be a bad idea, just for the piece of mind. I know this is a horrible thing to have happen, but I think it would made much worse if you were to just cover the hole and refill with fluid, thinking everything was going to be fine. Then a few hours later... BAM!
If it were me... I would try to pull out any pieces that I could possibly get to. Then try running a quart or two of fluid through the case, with the drain plug out, and allow it to drain. Inspect that and see what comes out. If you can take the pieces and make up the same area of the hole, then you should be good. If not.... there would be a 50/50 chance the other pieces are still in the case or laying on the road, were the accident happened. For me... all bets would be off and I would just have to find a way to get that tranny out, myself.
I hope everything works out for ya bro. I know this is a tough time for ya, so if you have questions or want to throw something out there, for suggestions, feel free to them at us. If you just want to have someone to "vent" at, you can always shot me a PM.
I had the sunroof rip off on the freeway on my Grand Cherokee, and they coverd the replacment under "act of god" 
)