OK I have seen a few statements here that really miss the pall.
let's go through them:
1) CDPR can deactivate the GMG codes.
For this to happen they have to know where they got the keys from. They don't. It is also highly unlikely that they will if GMG are telling the truth, when they say they got them through a legitimate retailer. The information will then be part of the deal struck between GMG and the 3rd party reseller. A deal they are under no obligation to divulge (unless under some provision of an earlier deal with CDPR).
In short: No they can't.
2) GMG can only have gotten their keys by getting them from a regions pricing them lower than in the western world or through other more nefarious means.
GMG lists the publisher as Namco Bandai. Steam lists the publisher as CD Project Red. This means that in negotiating with distributors CDPR has either been negotiating as publisher (higher cut of the final price) or developer (lower cut of final price)depending on the one they are selling to. These keys will likely be from the second group here as the first group likely only include steam as a platform (GOG is CDPRs own platform or at least their affiliation is very tight). As we know from the recent situation with paid mods the split for steam goes thus: 25% to developer, 30% to steam and 45% to publisher. This will likely not be different for The Witcher 3 which means that CDPR gets 70% of the sales price through Steam. They really like this I imagine. Now with other distribution platforms I wager they will not get as good a deal. Through Namco the deal will likely only net them about 30% of the final price, maybe even as much as 35% (as Namco Bandai did not actually bankroll the game). Now here is the important bit: Namco Bandai is now sitting with 65% of the final price to distribute between themselves and their retailers. Depending on how deep the distribution chain goes their cut can be anywhere from 25% to 40% with the lions share probably lying in the 30-35%. If the guys were skilled enough they might have gotten that sweet sweet 25% (though the 30% is more likely) Leaving them with between 30-40% of the final price of the game. Now they could sell the game at full price and sell a fairly low number of the keys they have... or they can give their customers a deep cut in price. This will limit their own profit BUT will potentially draw new customers to the site. Seeing as people in the chain only actually get paid if the final product is actually sold (this is not potatoes) a middle man might actually be willing to lower his cut of the profit if he knows of a cut like this, seeing as the sale is practically guaranteed.
In short: There are legitimate ways to get a good deal on a product.
3) Unknown Source
This has been covered by others but I will include it here:
Green Man Gaming (the ones giving the low price) knows full well who their sources are. I am guessing here but I expect it is from Namco Bandai directly (though there are some pitfalls with this idea).
CD Project Red (the developer) don't know the source of the keys. This is natural. They likely don't know where the boxes in my locale store came from.
In the aftermath of the launch they can probably track some of the keys and find out who the sources were.
Now on to the situation itself. If we assume that everyone are telling the truth (which I think is likely) then the facts are as follows:
CD Project Red don't know where Green Man Gaming got their keys from.
Green Man Gaming got their keys from a legitimate distributor.
Green Man Gaming and CD Project Red were in negotiations to get the game on GMG, but the deal fell through.
Both GOG and Steam are both running their own deals at the moment with steam having cutting the price by about 25% (where I am).
Now we get into speculation territory. GMG is well known for having deep cut sales all the time. Their rebate codes are almost legendary. For a system like that to work they almost certainly have to be taking most if not all the rebates out of their own cut.
Steam is similarly known for offering nice deals even for new releases if the distributor is willing.
CD Project Red has long been known as a trustworthy and consumer oriented company.
So why could GMG and CD Project Red not come together on a deal? The reason I wager is that GMG made their wish to give a good apparent. Now CD Project Red was probably not against this on principle. They are probably in favour of a good deal (though The Witcher 3 is their most ambitious project yet). They just want people to get the good deal from them. If GMG were to get The Witcher 3, I bet you one of the stipulations, they would have to agree to, was that, they could not discount the game for... a month? This would of course not be something that GMG could agree to, especially when they probably knew that both GOG and Steam would be running promotional deals. If GMG were to sell the game with no promotional deal they would not get any sales let alone traffic for their site (CD Project Red likely knew this as well). At this point it is worth noting that where I am the 35% rebate offered by GMG only allows the price to match the deal I would get from Steam. With no discount they would not be able to compete at all. So they found a different solution. By using the fact that CD Project Red would not cut off all other streams of revenue to get people to GOG, GMG would be able to find keys elsewhere. So by likely moving from the digital arena to the physical one they would be able to find keys for their customers. This of course is not a nice thing to do but neither was blocking out third party store-fronts like GMG and I expect GamersGate and Desura. CD Project Red would of course not block off Steam.
In many ways I feel that this is a situation with CD Project Red trying to control the market, failing and then being petulant about it.
So where should you get you copy from? Well if you want the developer to get the biggest cut you go for GOG. If you want some nice fuzzies in you stomach, as you buy, you go for The Humble Store (it is a good cause after all). If you have both the previous games Steam, it will be the cheapest. If you don't have the previous games, GMG is cheapest but you have to live with the somewhat bitter taste in the mouth, coming from the developer not approving. So, make you choice.
