Use Profile Manager in OS X Server to create a Custom Settings payload. Type in the preference domain name "com.apple.Safari", and add a ManagedPlugInPolicies key as described below.
Key | 
Type | 
Content | 

---|---|---|
ManagedPlugInPolicies | 
 Dictionary | 
Information for each managed plug-in is stored in this dictionary. The key is the plug-in's bundle identifier and the value is a dictionary with plug-in info, described below. 
 
 Common plug-in bundle identifiers include: 

| 

Plug-In dictionary

Each plug-in information dictionary can contain the following keys:
Key | 
Type | 
Value | 

---|---|---|
PlugInFirstVisitPolicy | 
 String | 

 Optional. Determines plug-in policy for the first visit to websites that uses this plug-in. Based on this policy, Safari will allow the plug-in to run, block the plug-in from running, or ask the user if the plug-in should be allowed to run. 

| 

PlugInPreventPerSitePolicyChange | 
 Boolean | 
Optional. If present and set to true , the user may not change plug-in settings for websites defined under PlugInHostnamePolicies . | 

PlugInRunUnsandboxedOnFirstVisit | 
 Boolean | 
Optional. If present and set to true , a plug-in can run in unsafe mode when visiting a website for the first time. The default value is false . | 

PlugInHostnamePolicies | 
 Array of Dictionaries | 
Optional. This array stores settings for individual websites. The dictionary format for each website is described below. | 

Website dictionary

Each website dictionary can contain the following keys:
Key | 
Type | 
Value | 

---|---|---|
PlugInHostname | 
 String | 
The hostname of the website. | 

PlugInPolicy | 
 String | 
Determines plugin policy used when visiting this website. Allowed values are the same as the PlugInFirstVisitPolicy key described above. | 

PlugInRunUnsandboxed | 
 Boolean | 
Optional. If present and set to true , the plugin is allowed to run in unsafe mode. The default value is false . | 

Learn more
For a sample of the Safari plug-in settings, you can look at the source of this sample configuration profile.