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Note that the version of SQL Developer that ships with Oracle 11g is rather old. In my opinion, the best approach would be to download the latest production release:
Choose Windows 32-bit - zip file includes the JDK1.6.0_35 and unzip it into an empty directory. It will run on either 32-bit or 64-bit Windows systems and already contains the correct JDK, so you avoid having to worry about that.
The security issues don't involve Java 6 and are limited to the version that run in your browser. The 1.6JDK that ships with SQL Developer 32 bit windows distribution is unaffected.
You can run SQL Developer with Java 7 but you will get a warning message on startup that we don't support it. Which we technically do not, for now.