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It is currently not possible to set group morphisms from generators (see also question 3157). Nevertheless, you can build a morphism by explicitely give the corresponding map

sage: flip = PermutationGroupElement("(1,2)")
sage: g = PermutationGroup([flip])
sage: id3  = Matrix(GF(3), 1, 1, [1])
sage: flop = Matrix(GF(3), 1, 1, [2])
sage: k = MatrixGroup([flop])
sage: H = Hom(g,k)
sage: h = H(lambda x: flop if x == flip else id3)

And then

sage: h
Generic morphism:
  From: Permutation Group with generators [(1,2)]
  To:   Matrix group over Finite Field of size 3 with 1 generators ([2],)
sage: h(flip) == flop

In 3157 you can see how to do this for arbitrary finite groups using the Cayley graph.