My 2 cents on how to "fix" the AQ tier issue...
My suggestion is let AQ play out as normal... let the ally's in the wrong tiers keep the milestones they are getting, but when they are "fixed" also give those ally's the proper milestones they should have gotten from their proper tier. For those not effected by the glitch.. give them a reward package with map 3 crystals (IE what most are getting because of this).