For the government, this will be a small price to pay. The Bitcoin community is very small and any action against it won't invite a backlash.
If they feel they can safeguard people from losing money by doing this, they might go ahead.
For now, Bitcoin is small, and more so in India. But
these charts from Localbitcoins show a global trend of growth. And India is one of the countries with the steepest and most sustainable-looking growth, and has all the ingredients to be a leading Bitcoin nation in the coming decades.
That means: The opportunity the Indian government could miss is still a future one, but it could be soon a big one.