[Fatt_Shade]

Here`s fix for you.
Game folder/sessions/addon/ses.kfs/items.txt Open ses.kfs with winzip/winrar , and items.txt open with notepad. When find and open file ctrl + F , and type marshal and find that item, it will look like this :

marshal_baton {
  category=o
  image=heroitem_baton_marshal.png
  hint_config=object_item
  label=itm_marshal_baton_name
  hint=itm_marshal_baton_hint
  information_label=itm_marshal_baton_info
  maphint=
  mapinfo=
  atoms {
    1 {
      atom=
      lu=template_item_mb
      label=
    }
  }
  price=65000
  maxcount=0
  level=5
  race=human
  use {}
  fight {
    {
      filter {
        belligerent=ally
        race=human
      }
      pbonus=moral,1,0,0,-100,0,0
      dbonus=
      rbonus=
      attack_on=
      attack_off=
    }
  }
  mods {
    leadership=count,1000
  }
  propbits=regalia,rare
  params {
    upgrade=officer_baton,colonel_baton,general_baton,marshal_baton
  }
}

Change part in filter to look like this :

      filter {
        belligerent=ally
        ~unit=droideka,droideka_guard
      }

With this you included all races, except droids, because they simply cant have positive moral due to mechanic nature. Save change then close file, save changes to archive in winzip/winrar and close archive. Start game check if it works now, and give moral to all units.
If not go back to file ,and return original settings. Hope i helped, good luck

After thought : you can change leadership to +2000 , or moral to +3 , but that would be to much