Oracle’s JVM is only installed in one location. You’ve been misled!
As you’ve noted, the Java commands in /usr/bin are symlinks to binaries in /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands. The binaries within that directory are stub applications that determine which Java VM to use*, and then exec the corresponding real binary within that VM version. This is why all of the binaries within /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands are almost identical in size, despite the fact that you’d expect them to be implementing quite different functionality.
You can see this in action by using dtrace:
mrowe@angara:~$ sudo dtrace -n 'syscall::posix_spawn:entry { trace(copyinstr(arg1)); }' -c "/usr/bin/java -version"
dtrace: description 'syscall::posix_spawn:entry ' matched 1 probe
dtrace: pid 44727 has exited
CPU ID FUNCTION:NAME
8 619 posix_spawn:entry /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/bin/java
The given dtrace invocation prints out the path argument to posix_spawn when it is called by java -version. In my case the stub application has found Apple’s Java 1.6 runtime in /System/Library/Java/JavaVirtualMachines/1.6.0.jdk and is invoking that version of the java command.
The stub binaries also have another benefit: when they detect that no Java VM is installed they will prompt the user to install one.
As for the CurrentJDK symlink, as best as I can tell this for sake of backwards-compatibility with the past when Apple was the only source of the JVM on OS X.
* A combination of factors are considered when determining which Java VM should be used. JAVA_HOME is used if set (try JAVA_HOME=/tmp java). If JAVA_HOME is not set then the list of all virtual machines on the system is discovered. The JAVA_VERSION and JAVA_ARCH environment variables are used, if set, to filter the list of virtual machines to a particular version and supported architecture. The resulting list is then sorted by architecture (preferring 64-bit over 32-bit) and version (newer is better), and the best match is returned.