You bring up an interesting point. Tolkien was a great admirer of northern European folklore, in particular Beowulf. The anonymous author of Beowulf wrote the epic poem at the time Christianity was slowly spreading throughout England. It is almost certain that this author was a Christian himself. He used the poem to sanctify the best of the old pagan ways. This sanctification is in the tradition of St. Augustine's argument that Christianity could be compatible with a post-Roman world. Clement of Alexandria also argued along these line when hed said that the pre-Christian paganism of the Greco-Roman world was a "prepatory teaching for those who [would] later embrace the faith."
Just because something is pagan doesn't automatically mean it is evil.
It would be too far afield to get into Beowulf on this thread, but the fact is that the epic is an uneasy amalgamation of Christian and pagan elements. As the story progresses, the author seems to drop the Christian elements along the way and revert to a raw barbarism. As an epic poem it is wonderful, but as an attempt to "baptize paganism," it is a mixed bag at best. Nor would it make sense for Tolkien to try to repeat the process some 1400 years later. It may not have been his intention, but the result of his work has been to resurrect paganism, not baptize it.