I was one suggesting both a bracket system and that the rewards don't really matter, so I suppose I ought to be happy with the proposed solution. However, could I suggest a nominal reward for being a bracket winner that does not include gems and does not scale at all? For example, the winner of each bracket gets a bonus X glory, Y gold keys, or Z new guild war troops. And this X, Y or Z number would be fixed for all brackets (and low enough to be relatively trivial), with the existing reward table otherwise unaffected.
I play in a city-wide sports league that has a "fun first, winning second" motto, but the winner of each league, each season gets free t-shirts (whether they play in a rec division, intermediate or advanced). It's a lot of t-shirts, but it doesn't devalue the t-shirt economy in my town, or by analogy to your Gems economy comment, the actual economy. And getting even a crappy t-shirt can be a point of pride.
Just a thought...