Yes. It's not as easy as it used to be, but I'm almost over complaining about JAMF needlessly deprecating MCX. Almost...
Best granular way to do it now-a-days is a custom config profile payload. Start by creating a fresh profile and trusting the site the way you normally would - install the plugin, visit the site, and trust it. Then you can go into Safari's Preferences > Security > Plug-in Settings and adjust the settings as needed. Once this is set, grab a copy of ~/Library/Preferences/com.apple.Safari.plist from that Mac and convert it to XML:
plutil -convert xml1 /path/to/copy.plist
At this point you can open up the XML-formatted plist file and edit out all of the various keys other than ManagedPluginPolicies (note that this would capture any other plug-in settings you've set, which is why I recommended a fresh profile), and save the resulting "plist snippet". In your JSS, create a user-level Config Profile, and go to Custom Settings. Set your Preference Domain to com.apple.Safari, and upload the plist snippet you made.
Keep track of your snippets; if you needed to make a simple edit, it's easier to start from the snippet and just update a version number or URL. We manage several plugins in way - it allows us to apply the current gatekeeper settings via SUS and, on a site-by-site basis, allow outdated plugins to run (or run in un-sandboxed mode, which is un-safe mode).
HTH.
