There's a new post up by Chris Metzen that makes an attempt at explaining the interesting quandary of the new Draenei lore. It's a fairly long post, so I'll summarize...
- The change in the Eredar/Sargeras encounter was an accident, caused by not reviewing the older lore.
- Sometimes you need to be a bit flexible with the world's history in order to "broaden the scope and accessibility of your setting."
- They're going to run with the story as it currently is on the Burning Crusade site. They feel it's a stronger story and have already started to build around it.