You could try this indexing method:
A = torch.tensor([range(1,11), range(1,11), range(1,11)])
B = torch.tensor([[1,2], [2,3], [3,5]])
A[torch.arange(A.size(0)).unsqueeze(1), B] = 0.
print(A)
> tensor([[ 1,  0,  0,  4,  5,  6,  7,  8,  9, 10],
          [ 1,  2,  0,  0,  5,  6,  7,  8,  9, 10],
          [ 1,  2,  3,  0,  5,  0,  7,  8,  9, 10]])

but I’m unsure if you would see a speedup compared to scatter_.