How do I disable inline PDFs in Safari 5.1?
I don't know of any way to disable inline PDF viewing, but option-clicking on a link will force a download instead. Not exactly what you asked for, though...

What's interesting is that some PDFs actually get downloaded instead of previewed, so that could be a starting point for a hack: http://www.jbc.org/content/279/1/686.long (click on the link 'Full Text PDF').