I would imagine that possibly somethings may be grandfathered in, but others won't on the grounds that it's not trackable (because it's not being tracked now).
For example, even if 25+ people in the guild have an achievement for downing Heroic Arthas, there's not any possible way -in game- to "prove" that it was done as a guild, or under the current guild tag. EVEN having a realm first achievement on 25 people in the guild, although I'd imagine any rational person would agree that it was surely done as a guild, it's still only circumstantial evidence, not necessarily "proof". Just like being exalted with the waterlords is a pretty good indication that you've done MC more than a few times, it wasn't enough to qualify for the complete MC achievement, as it's not direct indicator.
There's not a huge amount of information yet how it will work, joining a new guild they said you would lose some of your rep but not all of it. You'll retain some of it based on ... something. Possibly the fact that you've killed Arthas on heroic, irregardless of whether or not the rest of the guild has may boost the guild's "Exp" by 1 or whatever, in which case in the above scenario, you'd likely get "partial" credit for having done it prior to the system being in.
Somethings will obviously be "grandfathered in" such as completing guild achievements which will (presumably) boost guild rank/score. One reported achievement (that is not yet in beta) is to complete 10,000 quests as a combined guild. I can't imagine too many guilds that won't have this completed, my guild will have it with just 3-4 people. The guild should get this automatically when the system goes live, just like when achievements came out, you automatically already had "Complete 100 quests" etc etc
TLDR: Somethings will count some won't and for the next two years we'll hear people say "but my guild did X in wrath, why doesn't it show on our achievements qq"