We've discussed allegory before but I can't for the life of me find the thread.
Anyways, JKR's been known to insert social commentary about bigotry and what not into the series, Lupin for instance. I reckon Stan Shunpike is another occurrence of this, the government has to be seen to be doing something so they pick up anyone showing the first sign of connection to the enemy.
In real life these days it is Muslims, rather than Stan, but the same principle applies. Look at Abuse Ghraib and Guantanamo Bay. Gotta be two or three actual terrorists in amongst the hundreds of people picked up for no better reason than being a male Muslim of fighting age.
The innocent aren't released without massive pressure however, because if massive numbers are found o be innocent it makes the government look incompetent. What little public confidence is left in the governments course of action would be gone, and they can't afford that if they want to keep their powerful offices. It was lack of public confidence that brought Fudge down and put Scrimgeour in in the first place.
I know I'm gonna take heat for this one, but I felt it was worth drawing the comparison.