Yeah, Hunter runes definitely lean Horde.
As far as Alliance favoritism goes, this complaint will disappear almost entirely next phase when Horde has a teleporter right to Gnomeregan’s doorstep but Alliance has no such thing to SM which is also placed in a capital city starter zone.
Then in Phase 3 they will get Rune of the Guard Captain with no Alliance equivalent.
Overall, SoD is going to turn out to be Horde favored and the blip with the runes will be a distant dream in a few months.