Mainly they raise three points:
1) PANTHEISM AND REINCARNATION.
2) RITUAL SUICIDE
3) CHILD MOLESTATION
I would like to put forth my own reply, for what it's worth.
Item 1 - As Christians there is an obvious answer to this concern. When I refer to myself as a Christian that means I believe in the Bible, and the Bible is very clear. "“You shall have no other gods before [or besides] me." (Exodus 20:3, esv) This is the #1 of the Ten Commandments. As a Christian I believe that there is but one God in heaven, and that 'the heavens' is not God. As a Christian I also believe that there is only the resurection of the dead to stand before God on the final day, there are no 'extra turns'. "And just as it is appointed for man to die once, and after that comes judgment..." (Hebrew 9:27, esv). As Christians we cannot be 'double minded' - just as a house divided cannot stand, nor can a man be double-minded (or divided of mind) and still be able to serve God.
Item 2 - I am not God, therefor it is not up to me to determine when I am no longer of use to my Lord. There are a lot of Christian teachings concerning suicide and I don't think I need to beat this horse. No where (that I can find) in the Bible is suicide condoned, and therefor - where my desire to be like a samurai, and the ways of the samurai may contradict the teachings of the Bible, I must conform my thoughts, beliefs, and actions to the Bible.
Item 3 - This is just plain sick in my mind. First and foremost as Christians we are to submit to the rulers that God has established over us (so long as the very same do not 'encourage' us to contradict or go against God). The laws of the United States, and most (if not all) of the world agrees. This is strictly forbiden and there are consequences for such actions.
I consider myself a "samurai Christian", but I am a Christian in the service to the Lord Jesus Christ first, above everything else. I have read Paul Nowak's book "The Way of the Christian Samurai", and I can find no mention of his support for the items listed as "concerns" (my term) mentioned in the aformentioned article. He is quite clear, and I agree, that what we are trying to espouse are the areas of the samurai that can show us ways of being more sincere, more dedicated, more 'single minded' if you will, Christian.
The enemy of our souls is crafty. It is not beyond him to insert strings of Truth wihin his web of lies and disception. This is true of anything we can encounter here on Earth.
I will wrap this up with two quotes from scripture:
We ask you, brothers, to respect those who labor among you and are over you in the Lord and admonish you, and to esteem them very highly in love because of their work. Be at peace among yourselves. And we urge you, brothers, admonish the idle,  encourage the fainthearted, help the weak, be patient with them all. See that no one repays anyone evil for evil, but always seek to do good to one another and to everyone. Rejoice always, pray without ceasing, give thanks in all circumstances; for this is the will of God in Christ Jesus for you. Do not quench the Spirit. Do not despise prophecies, but test everything; hold fast what is good. Abstain from every form of evil.
Now may the God of peace himself sanctify you completely, and may your whole spirit and soul and body be kept blameless at the coming of our Lord Jesus Christ. He who calls you is faithful; he will surely do it.
Rejoice in the Lord always; again I will say, Rejoice. Let your reasonableness be known to everyone. The Lord is at hand; do not be anxious about anything, but in everything by prayer and supplication with thanksgiving let your requests be made known to God. And the peace of God, which surpasses all understanding, will guard your hearts and your minds in Christ Jesus.
Finally, brothers, whatever is true, whatever is honorable, whatever is just, whatever is pure, whatever is lovely, whatever is commendable, if there is any excellence, if there is anything worthy of praise, think about these things. What you have learned and received and heard and seen in me—practice these things, and the God of peace will be with you.
So, in essence, I consider myself "Kurisuchan" (クリスチャン侍), or a samurai who has the mind of a Christian - or the mind of Christ. Just as I do not feel that any one person, or denomination, has it all perfect in their pursuit of Christ, I know there are things that the samurai of old may have done that I will NOT do. But that does not mean that there are things that they did, that were not praise worthy and worthy of being emulated.