You really believe that Militias are temporary? Al-Qaeda was a militia one day, ISIS when it was ISI was a militia, Hizboullah was a militia, Houthis were a militia. Khameer Rouge were a militia, Al-Maliki's overtly sectarian government that created the bed for Sunnis to take in ISIS in the first place was put in place by these militias.
What you are asking for basically is entire ethnic cleansing of Iraq. Killing of entire families, and this doesn't make you and ISIS supporters any different, they call for the same exact thing, only from the other side. If these militias you support have the same mentality as you then maybe they deserve each other.
My views of the militia's are that they will be useful in the fight against ISIS, the fighters of the militia's are Shi'ite Iraqis with most of them loyal to Iraq and Najaf school not Qom. Iran has it's own interests, they of course don't want the militia's to disappear as this gives them influence like an article stated, but that's unlikely to happen with the counterbalance of support provided to Iraqi gov and army from the west. Also unlike in other countries the Iraqi militia's won't fight the army. Remember Basra 2008, Mahdi army melted away from the city, same will happen here.
Abadi has called for the militia's to place themselves under Iraqi government command indicating his plans, their leaders will resist but the forces won't fight each other over it.
During Maliki the militia's were inactive, Al Arabiya and everyone was calling the army Maliki army so now they got their ideal situation, let them enjoy it as they wished for. Did you see the video I posted of Ali Hatem ? that explains their mentality, Safavid army is gone they're enjoying life with Dawla.
I don't call for killing innocent people, killing those who house and feed ISIS is a necessity to defeat the enemy which is inside the body ( country ). What is your issue with that anyway, it's treason during wartime, Europe used firing squads for such people.