If Doctor Eckelburg were God, surely it would make more sense for him to be frowning at Tom rather than 'with' him, because as we know Tom is waiting for his mistress, Myrtle, and from a Christian standpoint is committing the sin of lust. Yet, the use of the word 'with' corroborates the earlier point about Doctor Eckelburg's morally myopic eyes. This implies that instead of being a 'God' it is a morally compromised 'god', who, while looking over much of man's domain, also overlooks much of man's sins, highlighting the theme of moral decay.
