What is the Home Folder under /Library/Java for? I installed Java 1.7 from the oracle site.  Looking at my folder structure, there is /System/Library/Java and /Library/Java.  Under /Library/Java there is a Home symlink that goes to /System/Library/Frameworks/JavaVM.framework/Home.  I had to point my IDE (IntelliJ) to /Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home which is a little weird in that there is a Home directory, but that Home is not the same Home as is in Library/Java.

Did I mess something up in my install? Is this symlinked Home gonna mess me up at some point? 

The symlinked Home goes to Java 1.6 (which is what I believe Mavericks ships with?), but I have access to 1.7.
No you didn't mess anything up.  My Java 7 is in the same location as yours.  The Home symlink will not mess you up.

BTW you can add this to your .bash_profile to set your java home environment variable

export JAVA_HOME=`/usr/libexec/java_home -v1.7 2&gt;/dev/null`