That's a good idea you have there, making the plugin freemium so that all affiliate and donate links can be removed for those users who have bought this right.
In any case, which "SEO dropdown plastering the admin area" are you talking about? If you mean the admin area widgets either in the general WP admin dashboard or WP SEO settings pages, you can minimize them with a single click. Hover mouse on the title and an arrow appears on the right side. You can also order them around in both areas by dragging and dropping, so in WP SEO admin area you can for example minimize the unwanted ones and put them below all others. In the general admin area on top of the page on the right side just below the admin bar are Screen Options, from which you can hide widgets entirely.