It doesn't sound incompetent to me, there will always be false positives on that scale. Did they remove the OP's repo, or simply send them a message? If a legitimate email gets caught in your spam filter, do you switch email providers? Github and their process/humans/scripts don't sound like the incompetent ones in this scenario. I would be more concerned that my livelihood depended on such an over reactionary company.
"Hey boss,I tried cloning the Github repo of project X, but it says it can't be found, and I noticed our org page on Github is gone."
"Oh yeah, they sent us a message about the use of the word 'retard' in when referring to phase shifting."
"Oh, so they deleted our organization?"
"No."
"Oh? Well why can't I view it, weren't the projects public? What did you say to them?"
"I didn't say anything, I moved us to a different host."