Update: Adobe has instructions on their website: http://helpx.adobe.com/acrobat/using/display-pdf-browser-acrobat-xi.html
For some reason, the option to turn off showing PDF documents in the web browser has disappeared in Adobe Reader XI. This option can now be found under the Accessibility Setup Assistant.
1. Go to Edit > Accessibility > Setup Assistant…
2. Click Next
3. Click Next
4. Click Next
5. Click Next
5. Uncheck the box next to “Display PDF documents in the web browser”