This piece purports to be responding to this, but it isn't.  The Stonewall guidelines do indeed implicate academic freedom (for the reasons stated in the letter, which are ignored in the "response"), and the letter doesn't claim that academic freedom protects mistreatment of students–quite the contrary, as one of the signatories to the letter wrote previously.  The non-response does contain one accurate factual statement, when it refers to the attention given to these issues by "the leading blog in philosophy."  A shame Professor Bertram did not link to any examples from that "leading blog," for example, this.