I want to buy a Suzuki GSXR1000, Suzuki Thailand sells it for 799,000 baht and RedBaron in Bangkok sell the same 2011 model for 678,000 baht. What is different and from who should I buy?

Import or Proper dealer with Dealer backing. Choice is yours. With the Suzuki shop your sure of OK plates and green book if that worries you and factory service.
personally I have many imports. But it gets down to your wants

With any other motorcycle shop in Thailand I would probably tell you “Go direct to Suzuki and buy it from the Suzuki big bike shop”, but RedBaron in Bangkok has earned its reputation as solid and honest motorcycle shop not for nothing. RedBaron sells its bike with good warranty, and good service...

The difference of 100,000 THB can buy you a good amount of special modifications or a good protective motorcycle suit and helmet... or a week holiday with the wife on a tropical island...

Still you need to compare what they both offer, if I remember correctly Suzuki Thailand gives 2 years factory warranty... Not know the warranty of the RedBaron Suzuki... but you have to figure that out yourself.

Also keep in mind that within a few months Suzuki will introduce the Suzuki GSX-R1000 K12, which, according to rumors has many improvements over the K10/K11 model.