SmartGit, SmartSVN, SmartSynchronize and a lot of other Java-based (GUI) applications, e.g. Eclipse, hang on OS X 10.11 beta 3 / public beta 1 (El Capitan). They worked on previous OS X 10.11 beta versions.
It is discussed in following thread forums.developer.apple.com/thread/8776.
We will see whether Apple fixes it in a new beta version.
Update on July 27th 2015
The problem has been fixed by Apple with the release of OS X 10.11 public beta 2.