You seem to have not gotten the event where you try to recruit a scientist for the Institute and the MM stop you and essentially tell you to go to hell since this isn't a military and they don't have to follow what you say.
Did you also remember Des telling you not to fight the Institute with the MM if the RR option is available since she says that the MM would overthrow you if they found out you were helping synths. What exactly would you do if the MM supported genociding certain groups?