Though this doesn't answer your question about for loops, I would avoid using loops all together and create column-major linear indices to access into your matrix. Use sub2ind to help facilitate that. sub2ind takes in the size of the matrix in question, the row locations and column locations. The output will be an array of values that specify the column-major locations to access in your matrix.
Therefore:
A = ones(3); i = [1 2 3]; j = [3 2 1]; %// Your code
%// New code
ind = sub2ind(size(A), i, j);
A(ind) = 0;
Given that you have a table, you can perhaps convert the table into an array, apply sub2ind on this array then convert the result back to a table when you're done. table2array and array2table are useful tools here. Given that your table is stored in A, you can try:
Atemp = table2array(A);
ind = sub2ind(size(Atemp), i, j);
Atemp(ind) = 0;
A = array2table(Atemp);