In order to set a function (permission) for a site, you can add an entry to the tool registration xml, using the "function" tag.
Example:
<?xml version="1.0"?>
<registration>
<tool
id="sakai.importtool"
title="Import"
description="Import tool.">
<category name="course" />
<category name="project" />
</tool>
<function name="import.view" />
</registration>
You can then inject the SecurityService in your service, and call this method:
boolean securityService.unlock( functionName, resourceId )
example: securityService.unlock ("import.view", "2005012003")
which will return true if the current user has import.view permission on site 2005012003.