My opinion of the matter is that is seems that only the most politically-correct persons would argue this theory is racist. We are supposed to be scientists here, and when we are faced with evidence to support another claim, we must change our hypothesis. If some people were cannibals in this region, it follows that they did this for specific reasons.
Many of us have called cannibalism "barbaric." Sure, it is barbaric from our modern, Western viewpoint, but you have got to take this information in its context. Spirituality was very important among these peoples and in many cultures throughout the world a great person must be consumed in order for that greatness to continue existing in the world.
Even among the Greeks, known in the West for their wisdom and modernity, had greatly respected Queen Artemisia of Caria who drank the ashes of her brother-husband Mausolus every day out of love veneration for him. Instances of cannibalism such as this are seen throughout history and around the world.
Why should archaeologists then ignore historical fact and archaeological evidence of cannibalism simply because it may offend modern day peoples? This would be a gross violation to not only scientific truth but also historic truth.
Modern puebloan beliefs are certainly against cannibalistic practices, but we would do well to remember that in the past practices were different to those seen today. We do not have an Inquisition which burns people at the stake, though we definitely had that in the past. All of us have had less desirable cultural aspects in our ancestry, we understand this but our goal is to seek the truth as much as possible.