Trust me, I don't like GoDaddy either. But they're the most popular registrar, and I think it'd be foolish of me not include them. The market much, much larger than the subset of people like us.
Despite the vitriol for GoDaddy, I understand why you feel the need to include them. Don't let haters (no matter how justified their feelings) stop you from doing what you need to get a business off the ground.
If you don't like GoDaddy it would be nice for you to use your service to also educate users on which registar to use. By making GoDaddy the default, you give it your approval. What might be helpful is a page explaining the registrars, or simply selecting your favorite. No reason for GoDaddy to be the default if even you don't use them.
Most visitors that use these site don't click through on the affiliate links. The few that do end up paying for the rest.
And those few that click? They use GoDaddy...
I disklike GoDaddy as much as the next guy, but if you're in the domain business you can't ignore them.
(source: I run a similar domain site)