In the current release you can hide the download link, mask the URL, and hide the "new window" button. This of course doesn't prevent someone from downloading the original document, but it makes it more difficult to do so - they have to look at the page source to find the location of the file.
In the next version you will be able to block downloading in a way that means the true link to the document isn't printed anywhere. The document must still be publicly accessible, otherwise Google can't fetch it to convert it for the viewer, but you can keep that location a secret.
As for linking between the two (if I understand you correctly) this will probably not work. You can have links in documents if you choose to but linking from one document to another is a different matter entirely.