Before you answer, consider http://www.extremetech.com/computing/120981-github-hacked-mi...
A couple of years ago I was at one of the Github drink meetups. I asked if they were working on encrypted private repos (this was just before or around the time Github Firewall was introduced). A Github employee told me no… before adding that in his opinion source code was not valuable.
I asked him to clarify and he said imagine if Twitter had their source code leaked. It wouldn't be a big issue as Twitters success was built more on business execution rather than code. A valid point perhaps but small indie developers could easily be put out of business if the source code to their unique selling point or competitive advantage were to be made public.
I'm sure Github (and others) take security seriously, but given the above, caveat emptor!