Origin of cow slaughter in Bakrid

In the Judeo-Christian-Islamic tale, God asks for Abraham (Ibrahim) to sacrifice his son, Isaac (Ishmael) as an act of obedience. When Abraham was about to do that, God stops him and Abraham sacrifices a ram in its stead. This festival is celebrated as Id-ul-aza where an animal is sacrificed for God's blessing. Killing rams for God's blessing is a prevalent practice.

However, in India, cows are killed instead. How did this come about?

In scriptural teachings, eating cows is discouraged.
عليكم بألبان البقر و سمنانها ، و إياكم و لحومها ، فإن ألبانها و سمنانها دواء و شفاء ، و لحومها داء
... The milk of the cow contains healing, its fat is a medicine, and beware (iyyakum) of its meat, which causes sickness..
(Hadith: Mulaikah bint 'Amr, Tabarani, Ibn Mas`ûd, Mustadrak al-Hâkim. Declared Saheeh by Shaykh Albani (rahimahullah) in Silsilat as-Saheehah (1533) and Saheeh al-Jami' (1233))

Clerics point out that Muhammad never ate beef.

This is strange. How did this practice come about for Id, while violating their own religious scriptures?

The answer lies in the teachings of conservative Islamic scholar, Ahmad Sirhindi (1564-1624 ACE). To humiliate the Kfirs (infidels), in addition to levying Jizya, cows must be slaughtered as a symbol of political domination over Hindus who worship them. Source: Shaykh Ahman Sirhindi: An Outline of His Thought and a Study of His Image in the Eyes of Posterity  

For similar reasons, dogs were tortured in Persia, since they were cherished by the Zoroastranians & Yazidis. Source: A Persian Stronghold of Zoroastrianism by Boyce, Mary.(1977) 

In Arabic, Baqara means cow (not to be confused with the Hindi Bakra for goat).

That's how Bakr-Id came about.

Until 2015, there were copious media reports on the 'barbaric' animal slaughter festival in Nepal, but not a squeak on Id or Thanksgiving. In 2015, Nepal ended the animal sacrifice festival. 

References:
Learning from @TrueIndology's posts

Earlier research