Yes, this is possible, by default the javafx_scenebuilder-2_0-windows.msi installs to all users and tries to registry some fonts etc.
This can be avoided by running the following command. This will install a link to the Desktop, when it is run Scene Builder will install, just click Ignore on all the warnings about failed font installation.
msiexec /ju javafx_scenebuilder-2_0-windows.msi