Websense.com came up with a creative solution to help limit the PDF security flaw using Atomic Browser.   If you are concerned about the exploit,  create an Ad Filter to block all PDFs.

Directions:

1. Click the settings gear icon
2. Click “Settings”
3. Click “Ad Block Settings” and then “Edit Ad Block”.
4. Click “New Filter” and then enter: *.pdf
5. Click “Done” and “Save”.
6. Click “Ad Block” at the top-left corner  to go back to the main screen.
7. Click on the “Enable Ad Block” switch to turn it on.

This will work while you use Atomic Browser.  However, you still need to be careful of links from applications which automatically launch Safari (Mail, SMS, Twitter, Facebook, etc)