Ahh, i think I know why - the plugins files are loading before functions.php, and the call in the slimstats plugin doesn't use an action/filter hook so it executes immediately (which is why $pagenow isn't available). With the filter being added in your theme, the call from the plugin happens before the filter is exists, so it doesn't modify the results of get_option().
The reason it works for me is that I actually wrote a plugin to use instead of the functions.php file for code that I want to keep around even if I change themes, and it is set up to run before any of the other plugins.
If you want to do the same and use a filter instead of modifying the plugin, which I would recommend, you can set up your own custom functions.php plugin based on this code: http://justin.ag/technology/wordpress-plugins/wordpress-plugin-custom-functions-php/.
Basically just create a custom-functions-php folder in your plugins directory, add the code from that link to a file called custom-functions.php and then include the filter from http://justin.ag/technology/activate-wp-slimstat-dashboard-widgets-in-wordpress-multisite/ in a file called functions.php in the custom-functions-php folder. Activate the new Custom functions.php plugin in your admin and you should be good to go - it should work as a site or network-wide plugin depending on how you want to distribute the custom functions. Nifty for other code too.