While I had used the Terminal command defaults write com.apple.Safari WebKitOmitPDFSupport -bool YES with success for a long while, it apparently was broken by the recent release of Acrobat 7.0.7.
However, by navigating to /Library/Internet Plug Ins, I simply moved the (updated) AcrobatPDFViewerPlugin to the "Disabled Plug-ins" folder. Relaunched safari, and relaunched Acrobat, and it seems like the choice is respected -- now PDFs download like they should.

