Sounds like bullsh1t story. Afghans seem to be the boogeyman in Pakistan. Inflation - blame Afghans, rising property prices - blame Afghans. Just like how Europeans blame immigrants for their incompetence, pakistani authorities are blaming Afghans for their incompetence. Every country needs a villian, USA has had blacks and now Mexicans and UK has eastern european migrants.
I agree that those Afghans who are involved in criminal activity should be brought to justice and Pakistan has every right to ensure the safety of its citizens but the fact is that the police is highly corrupt in Pakistan which I have experienced first hand and they will make up bullshit stories to extract money from poor people. Once I was in Peshawar a police officer stopped a rickshaw, and there was an Afghan guy inside it so the police sat besides him and blantently put drugs in his pocket and then arrested him that apparent crime. The police asked him for 500 rupees and they finally settled on 100 or 200 rupees and the police let him go. This was during Ramadan and in broad day light. Unfortunately "rishwat khori" is quite rampant in third world countries. On many occasions, the police are involved in bribe taking giving lands illegaly to people so its not only the immigrants but also the local police to blame for these crimes.
I doubt that 2-3 million refugees can make much of a difference in a country of 180 million plus.