There should be a plugin that goes into all of WPMU Dev's plugins and basically makes a 'global setting' so it removes that setting from the actual subsite settings. Ex: with the subscribe by email plugin, this plugin could make the global send rate, same footers throughout, etc. Pretty explanatory plugin. Basically a list of checkboxes for ones that should be only available in the network admin area. The unchecked will be available globally. This should work on all plugins even not network enabled.