I'm not sure what you mean by: But this is not true. What you expected is true and can be proven in Isabelle as follows:
lemma "transpose (χ i j. if j = k then c * (A $ i $ j) else A $ i $ j) =
(χ i j. if i = k then c * (A $ j $ i) else A $ j $ i)"
by (simp add: transpose_def)