<p>When a template is added using the add-template stsadm command, it becomes available to everyone when creating a subsite. Is there any way to make it only available when a site collection is being created?</p>

go to site actions -> Site Settings -> view all site settings -> site templates and page layouts and remove the site template from the list of allowed items.
Gary Lapointe may also have made an stsadm extenstion for it; check
stsadm.blogspot.com
Mauro Masucci
http://www.brantas.co.uk