If you're still beating your head against a wall as to how to configure this, this is what I've done and it works so far.
Create a Managed Preference
Display Name (in my case): Safari 6.1 Managed Plugins
Description: VOODOO
Apply Setting To: System Level Enforced
-pop over to the Definition tab-
Domain: com.apple.Safari
Key Name: ManagedPluginPolicies
Key Type: Enter Manually
What the happy horse crap is a union policy?! Don't check that.
-pop back to the General tab-
-Note that Key says what we entered above-
Paste in the XML JUST from the ManagedPluginPolicies key (below is mine, scrubbed)
TAKE CARE to keep the xml style and indentation proper!
<dict>
<key>com.oracle.java.JavaAppletPlugin</key>
<dict>
<key>PlugInFirstVisitPolicy</key>
<string>PlugInPolicyAsk</string>
<key>PlugInHostnamePolicies</key>
<array>
<dict>
<key>PlugInHostname</key>
<string>vpnng.company.com</string>
<key>PlugInLastVisitedDate</key>
<date>2013-10-24T15:15:42Z</date>
<key>PlugInPageURL</key>
<string>https://vpnng.company.com/</string>
<key>PlugInPolicy</key>
<string>PlugInPolicyAllowNoSecurityRestrictions</string>
<key>PlugInRunUnsandboxed</key>
<true/>
</dict>
<dict>
<key>PlugInHostname</key>
<string>vpn0.company.com</string>
<key>PlugInLastVisitedDate</key>
<date>2013-04-22T13:39:46Z</date>
<key>PlugInPageURL</key>
<string>https://vpn0.company.com</string>
<key>PlugInPolicy</key>
<string>PlugInPolicyAllowNoSecurityRestrictions</string>
<key>PlugInRunUnsandboxed</key>
<true/>
</dict>
</array>
</dict>
<key>net.juniper.DSSafariExtensions.plugin</key>
<dict>
<key>PlugInDisallowPromptBeforeUseDialog</key>
<true/>
<key>PlugInFirstVisitPolicy</key>
<string>PlugInPolicyAsk</string>
<key>PlugInHostnamePolicies</key>
<array>
<dict>
<key>PlugInHostname</key>
<string>file:///</string>
<key>PlugInLastVisitedDate</key>
<date>2013-10-24T15:15:57Z</date>
<key>PlugInPageURL</key>
<string>file:///var/folders/</string>
<key>PlugInPolicy</key>
<string>PlugInPolicyAllowWithSecurityRestrictions</string>
<key>PlugInRunUnsandboxed</key>
<false/>
</dict>
</array>
</dict>
</dict>