I know as given the history of MQM as party and its leader in Karachi cannot be ignored, but comparatively, they are still still ahead in term of loyalty --- not necessarily its leader though.
What we have Afghani refugees indulging in its expanded crime network alongside with MQM in Karachi, and provide platform for TTP which that group is on bent of destroying the infrastructure of Pakistan and damaging the economical ports of Pakistan. Unlike TTP, MQM is also invested on developing certain portions of Karachi for progress and their loyalty [not leader] truly goes to Pakistan because that's only their home, not India and certainly not Afghanistan either.
Pakistan is not home to Afghani Refugees, and that's why most of them are ungrateful at Pakistan, and their willingness to support TTP in betraying Pakistan as whole should be put into perspective.