If Fortification stops the critical then it stops the critical effect which includes losing your head.
Now however something that I have done with Fortification is little more flexible reading of it since they don't really cover multiple effects or special effects during a critical hit.
Trainz said:
Fortification: This suit of armor or shield produces a magical force that protects vital areas of the wearer more effectively. When a critical hit or sneak attack is scored on the wearer, there is a chance that the critical hit or sneak attack is negated and damage is instead rolled normally.
Fortification Heavy totally imunes to crits and sneak attacks.
Since this says
When a critical hit or sneak attack is scored on the wearer, there is a chance that the critical hit or sneak attack is negated and damage is instead rolled normally..
I've ruled that the player chooses which effect is removed. The actual effect of loosing your head is a special effect, then there is the damage the player chooses which to take...Which I state as "Special Effect" or "Critical Damage".
This also applies when Sneak attack is involved.
So someone hit by a Sneak Attack with Crippling Strike that scores a critical and their fortification holds gets a choice to drop one of the effects but not all. Basically choose one "Sneak Attack", "Special" or "Critical Damage".
This way Heavy Fortification doesn't negate the ability of rogues completely or the effects of epic feats like Death of Enemies, Dev.Crit and Overwhelming Crit, etc.
Most of the time I've seen player choose to stop the Sneak attack damage because they are afraid of the lingering sneak attack after watching the various rogues in the party dish it out since the campaign went epic just as the epic stuff came out in Dragon
Criticals IMC can very vicious due to "Special Critical Charts" taken from 1E and 2E. This way things like Regenerate is required. Plus I brought back the Sharpness effect (little brother of Vorpal).
Even with using it this way, I still have one player out of 5 that has never been killed since we started this campaign (just before 3E came out and switched over when it did) and most of the other character deaths were mostly spell based or stupidity on the part of the player as far as the way they play. Running from a more powerful enemy when the player was capable of teleporting to safety and getting caught in a very bad spell effect that dropped them due to Con loss or when they were about to seal off a section of the evil temple to stop the BBEG from escaping a place you cannot teleport out of by putting up a stone wall and the barbarian refused to leave the area...so for safety of the party and the world they wall him in, and he died due to an implosion spell as he tried to break a way through the wall.
Very rarely do I have players dropped due Crit's, but multiple crit's etc now that's a different story.
RD