Where is it going against God's words?
First there is the issue of free will. Second, a few of the parables Jesus told indicates death is a boundary, and if a decision is not made prior to that it is too late. Third, none of the Apostles (not even Paul) taught proxy baptism.
So you say free will because God went ahead and had the Latter-day Saints perform baptisms for the dead without asking each person beforehand if they wanted it? First off, Jesus set up a missionary program in the world of spirits to convert them to his gospel. This is why the Bible mentions that he taught to the spirits in prison and that he preached the gospel to the dead. I don't think all the dead have been taught yet and I don't believe that all who will be taught have died yet. Secondly, God does not necessarily seek the opinions of all people before he commands his people to do something. Just ask the Hittites, and the Amorites, the Canaanites, the Perizzites, the Hivites, and the Jebusites if God asked them for permission to destroy them. Lastly, as I continue to tell you over and over again, God does allow man to choose salvation and he also allows man to choose damnation. If man has not received the gospel in this life, He, being a fair God, allows all those who have not had the chance to receive it to receive it. Now it may be that they were deceived in this life and were led astray by false teachings and deception. Perhaps in the world of disembodied spirits they finally get the opportunity to choose without the false teachings and deceptions. However, since those who receive the gospel in the world of disembodied spirits still need to be baptized to enter the kingdom of heaven, and since they cannot be baptized as a disembodied spirit, God has set up in his church the doctrine of baptism for the dead that all will have the opportunity to hear and accept the gospel and have the baptism necessary to enter his kingdom. There is no lack of free will in the process. As I've stated before, each person will have the opportunity of accepting or rejecting the gospel and if they reject it, any vicarious baptism performed for them will be of no effect and they will have had the chance through free will to enter the into his kingdom or not. No coercion, no force, just an unaccepted baptism that is of no effect because they did not choose to accept the gospel.
Nowhere in all the bible does it teach that disembodied spirits have no choice. Why would Jesus go and preach the gospel to the dead if the dead have no choice in whether to accept it or not? Why would he bother?
1 Peter 4:6
6 For for this cause was the gospel preached also to them that are dead, that they might be judged according to men in the flesh, but live according to God in the spirit.
God is giving us all the chance to change our hearts if we never have had the opportunity to receive his gospel and reject it. This is the reason he preached to the dead.
I can't say that Paul never taught baptism for the dead nor can I see how you can make such a statement. I say this because we do not have all the teachings of Paul. The bible does not contain all that every prophet ever taught. But according to 1 Corinthians 15:29 he bolstered his defense of the resurrection by using baptism for the dead as an argument. He certainly was aware of the practice. Instead putting it down as a false teaching he chose to use it as a reason to believe in the resurrection. Would Paul have used a false teaching for a reason to believe in the resurrection? I seriously doubt it. Paul knew the teaching was true and from God.