I brought a MacBooK Pro with Retina a month ago, and I just ran the Kindle app on my new Mac a week ago. I was shocked at how bad it looked. The text that looks so good in Safari and Mail looked bad in Kindle. I have really found the retina screen to great for reading. I can use smaller fonts on the MacBook Pro than other computers.
I googled Kindle for Mac Retina, and I found a thread on the Kindle forums about it. The version on the App Store does handle retina screens properly. You have to download the version directly from Amazon. I downloaded it, and replaced the App Store version. It is very enjoyable to read on the MacBook.