To prevent the Cloud9 IDE from interfering with your web server, you must disable these services:

systemctl disable cloud9.service
systemctl disable bonescript.service
systemctl disable bonescript.socket
systemctl disable bonescript-autorun.service

Even with these services disabled, you will still be able to use the Cloud9 IDE to develop code.

If you now enter the IP of the BeagleBone, you will see the Lighttpd placeholder page:

If you get Error 404, then you've forgotten to perform apt-get update as I suggested. So, you can either do the update now or try using index.html instead.