As mentioned above, the Overlords can be seen as ironic symbols of the Devil. In an unexpected, but equally effective way, the Overlords bring about the end of humanity just as the Devil was predicted he would. Whereas the Devil, or the Antichrist, would have brought about much death and destruction before the final end, the Overlords bring about peace and prosperity, albeit for less than a century. In the end, humanity does degrade into violence and death, just as predicted in Revelations; and the shepherds of this end are the Overlords. Whether they are "evil" or not is a matter of perspective; they do the bidding of the Overmind and play a part in the end of humanity and the destruction of Earth.
New Athens is symbolic of the inevitable decay of a utopian society and the uselessness of peacefully attempting to combat those problems. For all its hopes of artistic achievement, the New Athens colony is ultimately impotent. Without struggle, without anger, righteous indignation, rage, or hate, artists have no fuel with which to produce great works. New Athens, in its false attempts to create minor inconveniences in life (such as using kitchens and bicycles), tries to create a utopia within a utopia. New Athens is a symbol of the broader utopia of Earth around it. Both are doomed to failure through degradation.
If the Overlords represent the Devil, then the Overmind is the closest thing there is to God. Certainly, the way in which the children of the last generation are incorporated into the Overmind is reminiscent of Christian descriptions of the Rapture, when the souls of the faithful are called into the Divine Presence, there to remain for eternity as part of the Holy Trinity. But, in theory, the Overmind is a thing of science; it should be capable of being studied, understood, and perhaps even destroyed. By placing the Overmind in a science fiction novel, there are certain constraints on how far a symbolic or allegorical comparison can be taken. Ultimately, the reader must accept the idea that, as transcendental as it seems to be, the Overmind is just another alien.