Sri Sri Swamiji has given a detailed explanation for this question:

Once a few police officers arrested a group of rowdies and took them along.  Suddenly, all their weapons fell into a nearby well by accident.  If they got  into the well to fetch the weapons, the rowdies would flee.  Not knowing what to do, the police officials consulted an intelligent person in the locality for ideas.  He said, ‘It is not possible for your people to get the weapons all by yourself.  You need the support of the rowdies too.  Offer them a few weapons in return for their help and they will be glad to help’.

The police officials followed this advice and together they ventured into the well to retrieve all the weapons.  No sooner had they retrieved all the weapons than they clipped the wings of the rowdies and shackled them.

 A Sadhu or Sanyasi is supposed to bring peace only with Ahimsa.   He cannot resort to violence in order to establish peace.  The Dharma of a king is different.  It has been decreed that the king should bring peace only through force.

The rule for the kings go as ‘sama, dhana bedha danda’. 

In Mahabharat, this dharma is beautifully depicted.  When the Kauravas refused to give the kingdom to the Pandavas, Lord Krishna who approached Duryodana’s court as a messenger initially requested him to compromise and make peace.  This is ‘sama’ [‘samadhaana’],  When that attempt failed, he requested that at least five villages be given to the Pandavas.  This is ‘dhaana’ or charity.  When that did not work either, he deployed all tricks and tactics trying to confuse the Kauravas.  This is ‘bedha’.  Eventually, he resorted to violence and war, which is ‘danda’ [punishment].

This is ‘Raja Neethi’ [rules / politics of the kings] and the rulers are permitted to deploy this tactic.

Crime in a society is attributed to the poor law and order situation and hence bad governance.  That is the very reason why it has been said in our Shastras that the king is burdened with the sin of all his citizens. It is the duty of the king to strictly enforce law and order and the citizens should always abide by them and fear the ruler.

Even if there is a single anti-social element amidst a number of calm people, he is bound to cause troubles to others. Although we may expect policemen to be present in the location before violence happens and prevent it from happening, in a non-ideal world, crime and violence do happen.  In such a scenario, it is for the law enforcement officials to meticulously curb the violence with an iron fist and in an unbiased manner.  The strict procedures in recruiting law-enforcement positions and their rigorous trainings are illustrations to this fact.

So, analyzing our story, mercy to the thugs will only create danger for many innocent people.