I know this is an old question, but I've encountered it too and just written a small plugin to help with it. Siddhartha's answer is almost right, but when I used it, it intercepted all web requests, including those to my index.html, and this seemed to move my app into Safari. What I needed was a way to handle only explicit requests, so I could open specific (external) URLs in Safari.
There are many similar questions about Phonegap, which appears to embed special handling for window.open with _system. That would be nice, but Cordova doesn't have this functionality.
In the end, I wrote a small plugin that embeds enough Objective C (closely modelled on Siddhartha's answer) but due to the magic of plugins, it can be executed on demand, using cordova.exec. I'd love this to patch into window.open to achieve the same functionality as Phonegap, but that'll be for another day, and it doesn't really affect this answer.
As far as I can tell, in modernish Cordova, this is the only viable strategy.