Ok, I'll have a look at this. Secondary I'll add a warning message if token and URL aren't set.
There are three different ways to activate plugins in a blog network:
1. Site Specific Plugins: Just add the plugin. Each user can activate and use this plugin on his own.
2. Network Plugins: This is a global activated plugin working for all blogs automatically. Activation and configuration are done by the network admin, apart from that the functionality stays the same.
3. Must-Use Plugins: Auto-activate the plugin for all blogs, configuration is done individually (as you described). To use WP-Piwik as Must-Use Plugin you have to create a single file in mu-plugins including mu-plugins/wp-piwik/wp-piwik.php.