Actually couldn't they just remove Akismet from the plugin download page since it comes included with the Wordpress install? That way you satisfy people who demand 100% GPL "free"dom. And you'd still have to grab the WP key to activate Akismet, but the plugin is no longer on the website.

Seems like it would be a simple solution. It's their product, they can put whatever they want in the initial install download. If a person hates non-GPL stuff so much, they can take it out of the plugin directory if they want.