I think any PCI or other auditor who doesn't flag "domains registered with GoDaddy" during an audit is doing clients a disservice, given all the bad stuff that's happened. I'm not sure how exactly you could flag it for a client, though.
http://www.tucowsdomains.com/tucows-domain-promise/ "A thoughtful, “registrant-first” approach to dispute resolution. Tucows’ approach to any domain name dispute begins with the firm belief that your domain name is your own. We also have a full-time, dedicated Compliance Team to make sure these matters get the attention they deserve. We will not allow your domain name to be used as leverage in a dispute. We will not readily “seize” your domain name under public pressure as other registrars have done."
eNom is the other one where I know some of their management. They have killed some domains in the treasury table of deny orders, rather than going through the full ICANN process, but are nowhere near as arbitrary as GoDaddy.