Sorry Rob, the feed doesn't have to pass through the alternator, and anyway, the diodes in the alternator are only the to convert the *alternating current* that the alternator generates into good old DC. Any DC feed you put in isn't going to go anywhere near those guys. The alternator is normally attached in parallel to the battery.
Fried electronics when jump starting cars these days is a very real risk. Most car manufacturers say you shouldn't do it unless you use special jumper cables with a dirty big supressor built into them, and even then you've got to connect and disconnect the cables correctly. Anybody noticed nice big sparks from old fashioned jumper cables when you connect or disconnect them? Electronics don't like that sort of stuff!
If you want to protect your expensive stereo gear from people jump starting your car then I would suggest either *not letting them do it* (you could perhaps keep a battery inside on the charger. Actually sounds like it might be getting a bit sad anyway if it goes flat that fast) or build in some meaty supressors and diodes into your stereo power supply system. This last one still won't protect the other electronics in the car though.
Good luck getting everything going again!
Derek
(list 6284, Mk1 S/N 00299 4GB blue [for sale]. Mk2 S/N 080000094 6GB blue)
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(list 6284, Mk1 S/N 00299 4GB blue [sold]. Mk2 S/N 080000094 20GB blue)