I would also like to integrate repository documents with Share sites, but so far, using the OOTB Share interface, the repository button (without search capability) is what we have. I haven't looked v3.4 to see if anything has changed, however. I haven't seen that you can create a link to a repository document from the Share document library, but that would be a nice feature.
Regarding deleting a Share site – you would need to copy those documents to the repository or another site if you wanted to save them.