Hunt left his jobs at the Royal Society and University College London after telling a conference it was difficult to work with "girls".
"Let me tell you about my trouble with girls," he said.
"Three things happen when they are in the lab: you fall in love with them, they fall in love with you, and when you criticise them they cry."
Many decried his remarks as sexist and unhelpful in an industry in which women struggle to be taken seriously.
However, Dawkins argued that he shouldn't have been forced out of his job by a "witch hunt" made up of "self-righteous" people.
He wrote in a letter to The Times: "Along with many others, I didn’t like Sir Tim Hunt’s joke, but 'disproportionate' would be a huge underestimate of the baying witch-hunt that it unleashed among our academic thought police: nothing less than a feeding frenzy of mob-rule self-righteousness."
Hunt apologised for the remarks, claiming they had been intended ironically, but the damage had been done.
Brian Cox also leapt to Hunt's defence, asking whether it was appropriate to force someone out of a job because of "ill-advised" language.
Speaking on The World at One on Radio 4, Cox said: "Is it appropriate to hound someone out of their position at a university or indeed, is it appropriate for the university to react in the way that UCL in this case did and ask someone to resign or else threaten to sack them?"
He added: "We do have a problem about these mobs - you call them Twitter mobs, descending on people who use language ill-advisedly and cause great professional ruin. I don't think that is the case although he felt that.
"To have a Nobel prize winner and - by all accounts - a great scientist and a good person being hounded out of a position at UCL, after all those years of good work in science, I think that's wrong and disproportionate."Reuse content