Award all the exact same prizes, complete with modifiers, again. But this time, give them to just the original tiers.
So the teams who finished 1-10 get two of the top ten items, two top 25 items, etc., while the teams who finished 11 & 12 get one top ten item, and two top 25 items, etc. In this way, the teams who Gree felt needed to be offered something extra for their wartime blunders get rewarded - but not as much as the teams who legitimately finished in the brackets we were all fighting for over the first 72 hours and 58 minutes of the event.
No one can complain about the prizes given out, because they're the prizes they were originally battling for in the first place.
Fair and remarkably easy to get done, all at no cost to Gree's precious bottom line.
And then, never ever again change the rules or parameters of a war during the war.