Ideally we would like to restrict delete and create link permissions by issue type to prevent certain users from deleting certain types of issue links.

The next option would be to separate delete link into its own permission separate from create link.

The last option would be an API that would allow us to override the rendering of the links in the issue page, and we would hide/show the delete icon with a custom plugin. I understand that's not completely secure but it suits our purposes.