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Graph editor seems to be working in sage 5.8 :)

The code you posted seems to work, except that you need to multiply rot_matrix by vector(vert_pos[i]). If you really insist on having tuples instead of matrices for the positions you can try changing

for i in vert_pos:
    new_pos[i] = rot_matrix * vector(vert_pos[i])

to

for i in vert_pos:
    new_pos[i] = tuple(rot_matrix * vector(vert_pos[i]))