Today, Apple updated Safari to 5.1 (6534.50).
In Safari 5.0 or below it's very easy to disable opening pdfs inline, you simply say
defaults write com.apple.Safari WebKitOmitPDFSupport -bool YES
and it never bothers you again.
In Safari 5.1 this no longer works. Does anyone know an alternative to prevent Safari 5.1 opening PDFs in the browser rather than as a download and then in Preview?