I wouldn't make it a full class, but I can see it as a PrC rather well.
The agiel would gain additional abilities with every other level, from merely causing damage (perhaps equivalent to an Inflict Light Wounds spell?) to additional abilities (nausiate, stun, ability damage (dex? due to nerve damage?), to save or die).
Other aspects are hard to exactly measure. In the series magic is not well known - let alone understood or used - outside of the reclusive wizards (additive or subtractive). So in that sense it might be considered a low(er?) magic setting. In a more D&D normal setting, I believe that the Mord Sith would have some ability to wield magic, although quite low - just enough to better understand it and thus better counter it.
I would expect a strong will save and perhaps a strong fort save (considering what their training likely put them through). Reflex would be poor, BAB would be medium. Leather armor suggests Light armor proficiency. No shields. As for weapons, just the simple basics: the agiel is basically a tiny sized leather club.
So we have:
HD: d6 (?)
BAB: 3/4
Saves: Fort, Will (Refl poor)
Skill Pts: 4 + Int
Profs: Simple Weapons, Light Armor, No shields
Specials:
1 Create Agiel
2 (counter spell as caster of your PrC level, no need to prepare spell ahead of time)
3 Nausiating Agiel
4 ???? (Sneak Attack, maybe? Or a rogue special? something else?)
5 Stunning Agiel
6 (counter spells as caster *twice* your PrC level)
7 Nerve Wracking Agiel
8 ???? (Sneak Attack, maybe? Or a rogue special? something else?)
9 Killing Agiel
10 (anti-magic effect on single individual)
I would make it so that it required a Rogue 3 (or Expert 3) to enter, along with a few other specials (gender: female, Special: watched mother tortured to death by a Mord-Sith, Special: to advance beyond first level must torture father or surrogate figure to death, you know, the basics). It would require a NE alignment, needless to say, although one could shift away from that later - losing the ability to advance to higher levels as a Mord Sith (rather like a Monk that ceases being Lawful).
That is only a rough sketch, however. I tend to think that - as magic saturated as D&D is - a Mord Sith equivalent should have some magic casting ability: either its own spell list (with most pain and ability damaging spells listed on it) or continued progression with a requirement as to the type of spells that can be learned if a Sorcerer equivalent.
Hmm, there is an idea. Take the Duskblade and similar Focused-Sorcerer construct classes and make a version devoted to pain and anti-magic based spells of up to 6th level. Then add in an Agiel at first level and make it so that the agiel replaces the somantic (and vocal?) components when it is used as a focus. Then add in some abilities at 5th for enhanced counter spelling, 10th for antimagic (as a type of enhanced riposte counter spelling), and something similar for levels 15 and (capstone) 20. Perhaps the agiel even becomes capable of dealing more damage as levels increase - a type of arcane sneak attack that deals little damage but can damage any non-construct, non-elemental creature it touches as a touch attack. Or maybe not?
I'm still brainstorming the idea. Does any of this help?