The settings in Yoast will have no effect on your ThirstyAffiliates links as ThirstyAffiliates hooks in prior to any template code loading for its redirection.
Your best bet is to hide this settings box from your affiliate links edit screens.
You can do this by:
- Logging into the backend of your site
- Wave your mouse over the SEO menu
- Click on Titles & Metas in the sub-menu
- Click on the Post Types tab at the top of the screen
- Scroll down to Affiliate Links post type and check the Hide box
- Save
You affiliate links will now not show the meta box from WordPress SEO