I used Zotero for academic papers with OpenOffice.org, although now I have switched to LibreOffice. It works just as well in LibreOffice. Like your wife, I depend on it for citations and references. Zotero is an awesome tool.
I don't have any programming skills, so I can't comment on the possibility of a Zotero plugin for Scribus. However, Scribus will happily import text from OOo or LO, preserving styles even. Scribus is designed for a workflow where images are created in bitmap or vector editors, text is created in a word processor, and all are assembled for layout in Scribus. Although you can certainly edit text in Scribus, it is not designed to be a writing tool.
Usually OOo/LO is all that I need for an academic paper, but I feel your pain when you have a lot of images. In that case, leave the images out of the OOo document, i.e., use OOo just for writing. All the citations and references created by Zotero in your OOo document will still be in the text after importing it into Scribus.