One of the problems with other commenting systems is what I call The Clean Slate Effect. If a troll is sucky on site A, then goes to site B, they start over with a clean slate and can continue being sucky.
Words benefits from the fact that it's web-Wide. If a user is terrible, they get silenced everywhere.
You're totally right (as was Paul Graham when he spoke about how Hacker News is evolving) that these sorts of systems get worse the larger they get. And that getting too big too fast is definitely a bad thing. Just look at Digg.
So I definitely anticipate badness down the road, but feel the code foundation is there to deal with it as it comes.