More of an FYI if anyone else needs to manage the Safari > Preferences > Advanced > Internet Plug-ins > "Stop plug-ins to save power" setting like I had to.
After saving a copy of ~/Library/Preferences/com.apple.Safari.plist with the checkbox selected (default) and then another copy with the checkbox unselected, I ran a diff on the two files to find that the modified key was:
<key>com.apple.Safari.ContentPageGroupIdentifier.WebKit2PlugInSnapshottingEnabled</key>
<false/>
true: checked
false: unchecked
This can then be applied using a custom Configuration Profile, MCX or the defaults write command. Tested in Safari v7.0.5 and v8.