It is one of those times that you relive all that has passed.
I came across my own solution i had shared with the community back then, more than 2 years ago.
http://wordpress.org/support/topic/plugin-google-analytics-for-wordpress-problem-and-solution-with-multisite-network-enabled-site
Time flies and time mosquitoes.
The solution is you need to edit the file wp-content/plugins/google-analytics-for-wordpress/admin/yst_plugin_tools.php at line 16
and replace the line
var $accesslvl = 'edit_users';
with
var $accesslvl = 'activate_plugins';
Cheers