Sure.
Heck, I was running three production sites for a while for various different entities inside out organization that didn't want to use the same one.
- for the company as a whole (which included IT, Maintenance, Training, and several other internal departments).
- one for an external user base who needed to interact with member of our staff from across the state.
- and one for another specific group of external users that needed to interact with members of our staff.
If your database is different and the url is different you can have as may sites running different code bases as your web server can house and serve.
