How do I disable scaling for specific apps on Retina MacBook Pro? Is it possible to set certain non-Retina enabled apps to not scale up (in other words, run at a native resolution) on the new Retina MacBook Pro?
SwitchResX is what you want. It will allow you to set application specific display sets.

SwitchResX is a commercial third party application, but it is available to try for free and for download. Probably because it is technically a hack to use the full resolution of Retina Displays, it appears to be unavailable on the Mac App Store.

By creating display sets for each application you wish to use the full native Retina Display resolution, effectively, you can disable the scaling for individual applications.