This is by far the weirdest thing I have heard of.
I am curious...
What brand/model of receiver do you have?
Does it have AUX in rca plugs, or does it have some kind of connector that you connect to?
What size fuse did you have in the first time (when it burnt up) and what was the smaller sized fuse you put in?
Without looking at it, I can almost guarantee that you have some stuff mis-wired...but you probably already realize that by now.
For the mini headphone jack on the computer, the tip is one channel, the middle is the other channel, and the base part is the ground.
If the only way you can keep you system from blowing up is to run it through an isolator, I have to believe that something is horribly wrong in your wiring to the stereo...not just slightly wrong, but horribly wrong.
I have connected all sorts of audio things, to all sorts of other audio things, and never has it caused a short (that is what happened to your mobo).
Why? because there is no power going through the line level circuits...a couple of volts max, barely enough to measure.
HOWEVER, if you have a positive ground vehicle/stereo equipment (like some european things) then you could have hooked 12v positive to 12v negative...that WOULD be bad for your computer.
If you have no idea what I am talking about, then you had better back away from the computer and stereo, and go get some help quick.
My guess is you have a HU like the pioneers with the multipin plug to add cd changers, and audio input...and instead of connecting the GND from the audio plug of your computer to the -R/L in on your stereo you connected it to something else.