There are several tactics and strategies to deal with these protests and the associated violence.
In the short term, refuse to talk any further. All avenues for discussions are over. Every reasonable opportunity was provided.
Do a media blitz in the rest of India with savvy Ministers and trusted leaders. Lay down the benefits of the bill again and again. Tout success stories. Spend political capital if needed.
In Punjab, look for sympathetic outlets such as Gurudwaras and make an articulate and strong case. Get your MP's out. They should be prepared to lose some popularity for genuine reforms.
Go back to the Supreme Court and make a more convincing presentation instead of the half hearted effort done the first time around. Parliament and the GOI are sovereign when it comes to making laws. If the government insists, there is really nothing the court can do. After 10 years of discussions and an ordinance to the effect, lack of consultations is hardly an excuse for staying implementation of the laws.
Now in the medium and longer term
This protest exposed one major flaw in Indian laws. Inheritance by a non citizen allows non Indians to own large amounts of agricultural land. This enables them to make an agricultural income in India and not pay taxes, indefinitely. Much of this income is off the books due to hawala and also enables tax avoidance in the country were the non citizen has migrated too.
Here are some specific suggestions:
When a foreign citizen inherits land, it must be sold to an Indian Citizen within 5 years.
Inheritance tax for non Indian citizens
Agricultural income tax if the land if held by non Indian citizens.
Land owned by non citizens should also not get free electricity, fertilizer or any other subsidy.
The benefits of no income tax on farming income should only accrue to Indian citizens.
Make another set of laws to define an escalation ladder for protests. Once police barriers are attempted to be broken or any violence ensues, an automatic response should be put into effect, that dismantles the protest and disperses protestors.
Any time a protest disrupts traffic, causes loss of livelihood or results in destruction of property, it is no longer a peaceful protest and the police and administration must have laws covering their actions to diffuse, disperse and arrest instigators. Peaceful, non disruptive protest is ok.
Simply discussing and notifying these laws will set the cat among the pigeons.
The Modi government thus far has signaled lack of conviction in this matter. It must do the opposite.