It only prevents applications downloaded from the Internet that are /completely/ unsigned (and only if the program that did the downloading marked them as such). Self signed apps will receive a scary warning, but can still be opened, while apps signed with an Apple-provided certificate will work fine (doesn't matter if they're distributed via the App Store).
This means that already-run apps will work just fine, as would apps that are acquired via physical media (such as CD/DVD/flash sticks).
The reporting has done a fairly poor job of explaining exactly what it restricts and how it functions, unfortunately.