I can't see how Valve is going to welcome this as a permanent purchase mechanism unless they're getting a cut.
On the other hand, perhaps their recent change to how Steam keys were distributed (i.e. they're not shown anymore, you have to link your Steam account) was part of some private agreement with Valve to allow this.
Here is another store that has been doing this for some time: http://www.greenmangaming.com/
Developers set the global price for their game. They can also set a unique price per store. All sales go through Steam, referral codes send a commission back to the store making the sale. For example, you're a developer with a game on Steam, $9.99, and you want to sell it on the Humble Store for a 24 hour sale, at $4.99. You set the Steam pricing coming from the Humble referral links at a 50% discount. Now, users browse the Humble Store, see the game at 50% off, click to buy, and get forwarded to Steam, or go through a Humble checkout that uses the Steam API. Valve takes the money, distributes a percent to the developer, and a commission to Humble. If Humble wants to send a part of their payment to charity, that's up to them.
Valve wants to encourage more user stores selling Steam games in the coming year. I imagine a new payment system will be announced in mid/late 2014 to accompany these changes.