GitHub Enterprise request
How to use GitHub integration with GitHub Enterprise
Heroku's GitHub sync features are hard-coded to connect to and use github.com at this time. If possible, you could manage this process with a deployment web service of your own that receives webhooks from your GitHub Enterprise service, retrieves the repository's sources and pushes them to the relevant Heroku application.
This would also maintain a higher level of security as the contents would only leave your infrastructure when being sent to Heroku, which also only happens over secure channels.