This isn't really that big of a deal. GoGamer routinely sells stuff at a lower price than market, and it's not really a big deal that they sell one game off site at a markup, or even 30 different games. The market is permitting them to do so. Eidos doesn't care, it makes their game look super important going for double it's retail value. Is the collector's edition scarce? Yeah, does it have to be? No. Do you think that having an extra 100,000 players with a special mount amounts to a hill of beans to anybody? No.
Everyone is outraged over the principle of the thing, but it really doesn't matter unless you are looking for the collector's edition, can't find it, and don't want to pay double MSRP for it. I doubt that GoGamer's allocation of copies was that high to begin with. Putting a terrible deal (double MSRP) on their website is a bad business move, so selling them at Amazon makes much more sense. You always want your portal to have good deals, not crappy ones.
The game industry at the retail level is a HORRIBLE business. Used games are the only place retailers generally profit, and if you are losing $15 a game at launch, as GoGamer claimed to have been, it is very signifigant. For every game you don't make your $5 on, and even lose $15 on, you have to sell four more, just to recoup losses. Making $5 on a game is not profit, that money is not a $5 that goes into your pocket. It is spent on rent, power, internet, staff, etc. They probably get to keep about $1 of that as profit, once their debt load is even gone, which it probably isn't.
Anyone who is pissed about this, and has never owned a retail game outlet, really has no room to speak.
Taking a loss on something means nothing to those not taking the loss, but to the one taking the loss, it's huge.
Kudos to GoGamer for doing what they have to do to remain profitable. (or get profitable)
If you don't like a price at retail, don't buy it. It's just that simple. I've gotten many great deals from GoGamer, so no complaints here.