It seems like you're viewing the problem as one of re-configuring your application based on the subdomain it is accessed from.
Given that your university specific data is basically user data - i.e. it will change as users sign up for and use your application, I think a better approach is to store all of that stuff in your database and then create a service for accessing it when you need to, rather than as part of the application startup.
I would write a simple and minimal service that inspects the subdomain and returns the university ID. (You'd need to inject the @request_stack into it (see http://stackoverflow.com/a/20502945/86780https://stackoverflow.com/a/20502945/86780), access the hostname of the current request and perform some sort of lookup.)
As for creating subdomains dynamically - I'd suggest that you configure your webserver to work with any subdomain (i.e. *.yourdomain.tld) and have your application figure out whether it's valid or not.
Basically, avoid writing server config dynamically. This approach is likely give you problems when it comes to scaling and tuning your application.