O problema está no node-webkit
de: link
The quickest way I found to run LightTable on Debian:
Copy the download link from LightTable site
Paste the link in a browser (or wget) changing the version from 0.6.0 to 0.5.9 (.../bins/0.5.9/LightTableLinux64.tar.gz)
The previous version does not throw the dependency problem.