Instant Death checks the toughness value of the model.
Rolls to wound are done vs. majority toughness in the target unit.
So, in your example - a S8 weapon firing at a Dark Artisan formation with the Haem closest to the shot would result in the Haem's toughness being 7, requiring a 3+ to wound, and, if successful (and considering armor/cover) he would then suffer an ID wound, not be allowed his FNP, and would be removed from play.