Yeah man, it didnt die, I killed... 
and it's also killing my pocket :
Anyway, I have evertying soldered to my arduino, it's not easy and practical to unsolder everything everytime I upload a sketch. So removing the LED is not a good option.
If you are sure about what you are saying, so the energy is getting out of the VIN pin (instead of getting in) and I expected this may be causing my arduino death.
Your idea about using the DC input JACK is amazing but only if you are sure that energy cant get out of it. Does the DC POWER JACK only accepts energy in? Are you are it does not allow energy to get out?
Also, are you sure that when arduino is being powered by USB, it can allow energy to go out in the VIN pin? I took a great look at google and didnt find anything to support this.