The short answer to this is, yes…sort of.
I do not think the devs meant what happened to the Alliance however they have admitted they write for the Horde first and fill in the Alliance to the story after and it really shows. Most of the Blizzard team has mentioned bias and if you look at the racials…well the rest is history.
But I don’t think Blizz hated the Alliance, just they liked the Horde that much more leading up to…well, what we have now.