Yes, the land transfer deal controversy in Kashmir was justified, because it allowed Hindu pilgrims to exercise their religion. The transfer allowed people to set up resources and shelter for pilgrims. This was a kind, humanitarian thing to do. Even though the transfer is not popular, and resulted in large protests, it was a kind thing to accommodate the Hindu pilgrims.
While the purpose of the land transfer deal in Kashmir was a good one, the deal was not justified. The desire to Hindu pilgrims have a place to live is obviously a good cause, but the government should have known that it would create political problems. Additionally, environmental concerns makes the land transfer not justified because if the best is wanted for all people in the region, a different solution would have been found.