You can add a key to your user.config: <add key="AllowDeletingChildSites" value="true" />
Then log in to site 1 on your installation, and go to administration -> site list -> site 2 (settings). At the bottom there should be a 'delete' button you can hit.
On the same page before hitting delete you can move to the "host name mapping" tab. If there are no host names mapped to the site, it will never be visible, so that is an alternative to actually deleting the site if you want to keep anything that is on that site without it being visible.
Hope this helps,