Except DND is and has always meant to be a team effort, not just something for a single rogue to handle alone. Therefore the suggestions for other solutions involving spellcasting.
My suggestion would be, to those playing in those Hi-stake games where fortification becomes a neccessity to survive (Seriously, suffering 12d6 damage for multiple attacks in a single round will cramp most Fighter's style), is to create an armour which instead reduces the amount of the critical damage inflicted.
SO rather than completely negating an ability, reducing the damage itself to an "acceptable" level (say reducing damage from a crit or sneak attack by 25% - 50% - 75%). Leaving the Max at 75% reduction means that the Epic Rogue sneak attack ability is still not a complete waste of time. The trick comes in making its cost match the benefit.
Just a suggestion...
that way you get to not create a whole slewth of epic weapons that penetrate fortification. Or you can retain them, to penetrate 5% per "+1", for instance.
The real problem is that the Heavy Fortification ability is far too cheap. IMO, even the moderate Fortification ability is too cheap.
Make Heavy Fortification a +10 Enhancement equivalent, and you'll see its use drop in the early Epic level, I suspect.