What action did the Government of India take regarding the merger of Manipur with India?

They disregarded the popularly elected Legislative Assembly and pressured the Maharaja to sign the Merger Agreement.

The correct answer is Option 2 - They disregarded the popularly elected Legislative Assembly and pressured the Maharaja to sign the Merger Agreement.

All the other options are wrong as the government did not ask the Maharaja to sign the merger agreement after consulting the Legislative Assembly of Manipur. Also, no referendum was conducted and even no diplomatic negotiations were initiated.

More information:

Manipur was a princely state with its own monarch, Maharaja Bodhchandra Singh, and a distinct political and administrative system.
It enjoyed a measure of autonomy under British colonial rule.
Maharaja Bodhachandra Singh of Manipur signed the Instrument of Accession with the Indian government shortly before Independence.
The agreement ensured that Manipur would maintain its internal autonomy.
In response to public opinion, elections were held in Manipur in June 1948, establishing a constitutional monarchy.
Manipur became the first part of India to hold elections based on ‘Universal Adult Franchise’.
The issue of the merger with India sparked sharp differences in the Legislative Assembly of Manipur.
While the state Congress supported the merger, other political parties opposed it.
The Government of India exerted pressure on the Maharaja to sign a Merger Agreement in September 1949 without consulting the popularly elected Legislative Assembly.
The unilateral decision of the merger caused anger and resentment among the people of Manipur which is felt till today.