In my last playthrough I disabled the bots and killed all of the Faceless in Buzzer's shop except for the Mindreader, who I talked to and persuaded to let Buzzer live. When I went to DC, the Commander allied with me. Of course, I also saved the injured Faceless w/ an advanced health hypo, helped them out at Foundry, and was diplomatic with the Faceless in the Institute. Granted, I also slaughtered the Faceless party southwest of the merchants in Core City.
So unless this is unintentional, I believe that as long as you talk to the Mindreader and either a.) let them kill Buzzer or b.) persuade them into letting him live, you should be able to become allied to the Faceless in DC assuming you perform well in the other checks.