GE gives us far more control, far more logging and auditing (which is the real key), as well as nice things like LDAP authentication that make adding and removing users from the system far, far easier to manage. There are real reasons to use it besides just wanting things in house, although for a software company who needs to keep their software secure you shouldn't use anything except Github Enterprise. We all saw the bug that happened just a few months ago- who knows how many people were using that maliciously before it was made public.

I will say though, there have been a ton of improvements in Github Enterprise. We rejected it after getting a trial six months ago, and gave the sales team a huge list of problems (it was kind of disgusting, actually). Since then they've actually addressed the vast majority of our list (certainly all of the high priority things), which prompted us to look at it again. We're pretty happy with that decision.

That being said, if you're too cheap to buy licenses for all of your staff then you shouldn't use the thing. That's not a Github Enterprise specific issue though.