I think all of the "Lego Store Exclusives" have been made available to other retailers, although most are only offered online.
Currently you can buy the Ewok Village from Target.com for the same price (5% cheaper if you use a Target card) you can get it from Lego.com.
I'm sure at some point you will be able to get the Ewok Village at MSRP on Amazon, you just may need to wait awhile. In fact most (all?) of the fall 2013 Lego Star Wars releases are only available on Amazon through 3rd parties for inflated prices (Umbaran MHC, Starhopper, etc.). Not sure if this is a contract thing with Amazon that new releases aren't sold there for a period of time or what.