The most viable explanation to atone for Dimmesdale's lack of realization about Chillingworth's true motives is that the time that Dimmesdale and Chillingworth move together in chapter 9, represents the period of time where we find Dimmesdale at his weakest and most vulnerable.
This vulnerability is caused by his obsessive fear of being found out; his mind has now reached a point where that is all that he can think about. Someone who has a secret to hide is too busy trying to conceal his tracks. Moreover, Chillingworth has not given any evidence whatsoever of being there for purposes other than helping. This is why it is so hard for Dimmesdale to point out exactly why he feels uncomfortable around someone who has presumably devoted himself to Dimmesdale's well-being.
This is also why in chapter XVII we find Dimmesdale acting quite surprised at the news that Hester gives him regarding having an enemy. Prior to that, Dimmesdale had said:
Had I one friend,—or were it my worst enemy!—to whom, when sickened with the praises of all other men, I could daily betake myself, and be known as the vilest of all sinners, methinks my soul might keep itself alive thereby.
When Hester confesses who Chillingworth really is the reaction of Arthur Dimmesdale is "dark", and quite upsetting, to the point where Dimmesdale says to Hester that he could never forgive her for hiding it. Yet, we also find out in this dialogue that Dimmesdale himself had no clue as to how he could have possibly missed that.
I might have known it!” murmured he. "I did know it! Was not the secret told me in the natural recoil of my heart, at the first sight of him, and as often as I have seen him since? Why did I not understand? O Hester Prynne, thou little, little knowest all the horror of this thing!"
Therefore, all that the reader can do is assume that it is the preoccupation with his secret that has rendered Dimmesdale blind-sided by everything going on around him, to the point of not recognizing his own enemy.