Actually I think this can be done on a per tracker instance.

In interfaces.py create a new login action that wraps the login
action in cgi/action.py.

This new login action checks to see if __login_name exits in self.form.

Then checks to see if self.form['__login_name'].value is a valid user.

If not, search for a user with a matching email address. If you find
one, change the value of __login_name to the user's name then call the
handler for the LoginAction class.

There is about 10 lines of replicated code from the top of the
handler for the LoginAction class to do this, but I think it could
work.

If it does, we should be able to reuse the logic as a patch to the 
LoginAction handler.