This isn't the first time we've seen Blizzard willing to put a strong counter to Resto Druids in the hands of a single class. (Arguments about Hunters/Druids being the strong counter to Warrior/Druids are kind of aside here - both comps still have Druids.) You don't see how this new damage type is the Druid counter? It's pretty simple -- Druids don't have a cleanse that works against Disease.
If Death Knights become a favored arena class, then the presence of Disease in the Arena could help provide solid reason to go Paladin or Priest over Druid. Of course, that assumes the disease effects are significant enough to matter. And cleansing all that Disease is still going to be a pain even for our Paladins: they can only cleanse one at a time, and they'd blow through quite a few global cooldowns trying to clear their partners.
I don't know if this dynamic was intentional, but I would find it hard to believe that Blizzard's ignorant of it. They tend to have an idea about what's going on. We don't know what new gear will be available to combat diseases (Resistance? Resilience?), and it's still way early to be hedging bets -- but introducing the Death Knight and their diseases should certainly mix things up.
Edit: I've not forgotten about Shamans, but I was mostly focused on Druids in this article. My apologies to any Shaman who issued a rightful reminder for the call out.