Haris-
The new method for completing BibTeX keys sounds reasonable to me. I don't think has disadvantages, unless BibDesk is able to return a search on more fields (sometimes I forget an author and have to search by keyword -- though I don't think either completion method offers this now, so I have to switch over to BibDesk anyway). And this change won't affect the ability to use BibDesk's own completion service. Seems like a good idea, off the top of my head.
One question: if multiple bib files are specified, ie via \bibliography{bib1,bib2,bib3}, I assume your script will get and search all of them?
-Alan