Automatic Transmission problems of the 2008 Subaru Legacy

I got off the highway on a secondary road on my way home, when after the second stop sign trying to cross the intersection the car stalled ,losing its gears with the engine running, but no acceleration. The check engine light went on,the mode driving light and the cruise lights blinking. I turned the engine off ,then on and I proceeded with the only gear left to a safe location. Luckily I was on a secondary road or I could have been rear ended and hurt or worse. The car was towed to the dealer who is telling me that it has to be reprogrammed due to a slippage(time gap between the 2nd & 3rd gear) ; he also tells me that the brakes are vibrating should I worry about damage to my gear box? at this point I am worried about driving the car even when it's fixed.