In principle, the sharing model should work like that. Everyone who has access to the Google Document should be able to edit the references. The references are part of the document so they should be editable.
However, once you share the final product as PDF you should be careful not to share the links with someone you don’t want have access to your references. That’s not an oversight. We had an option “export without markup”, see the discussion there: Plain copy without markup? What does it mean?
For technical reason we had to temporarily remove this option because it was broken and it’s currently technically not possible to fix it. We will bring it back together with a major update of the Docs plugin, which uses different Google APIs that make this feature possible.
For now, please refer to my tip how to remove all links from a word document in the thread above or remove the links from the final PDF before sharing it. Adobe Acrobat offers a way to do that:
https://answers.acrobatusers.com/Remove-links-document-q10878.aspx