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In a large weight attack, a double spend is created and tangle of transactions is build upon it ensuring that when the double spend is finally broadcast, the cumulative weight of it's tips outweighs the previously broadcast spend.
How does the Coordinator issued Milestones protect against this assuming that the double-spend tangle also references those Milestones going forwards?
Yes, the coordinator does protect us against these kind of attacks.
Let's call the honest transaction A and the double spend B.
If neither A or B are confirmed, the coordinator can only confirm one of them. If it would confirm both, his milestone would be rejected, just as any other transaction trying to archive that.
If A already got confirmed by the coo and the attacker adds weight to his own transactions, it can still not get confirmed by the coo. The coo is steady and never rollbacks his milestones, so for the coo the address is already empty ==> the double spend is deemed invalid and rejected.
