It probably wasn't the stereo that caused the alternator to go out. It could be possible that it was old and worn out, and the demand caused it to over work itself, but it still doesn't sound right. I would suggest a better battery (such as a recombination battery(gel batteries like Optima red tops)) and a capacitor so when the big bass hits, it doesn't drain the battery as much. Also make sure you got an in-line fuse for your B+ wire coming off the battery, just to be safe.