I don't think friendship between Mueller and Comey is alone enough to require that Mueller resign, just like I don't think friendship between Trump and Flynn entitled Comey to demonize Trump's suggestion that Flynn get some mercy after being fired. What does require Mueller to resign is that his appointment became tainted the minute Comey decided to wait until after that appointment to publicly reveal Comey had never been investigating Trump. Comey thereby made it impossible for Mueller to maintain the integrity of a Special Counsel.