I answered yes to the poll, but I don't think it is wrong for the pledge to the American flag to be said in Church. I don't think it is wrong because, as Jesus said in Luke 20:25, "'Well then,' He told them, 'give back to Caesar the things that are Caesar's and to God the things that are God's.'"
We do, in a sense, have a duty to our country to serve it. Part of serving it is pledging to, since we live here, respect serve and protect our country. I do agree with you that the pledges should be said in the opposite order. I've often thought about that myself.
