As mentioned in the Mixolydian's post, both "I disagree on his coming" and "I agree on his not coming" mean essentially the same thing.
Let's take a look at the whole sentence again:
I don’t think that he will come tomorrow.
The emphasis on this sentence's "not" is on "think". Everything after the "that" is just a description of what the speaker thinks. We can expand the contraction, apply emphasis, omit the sentence after "that" (for illustration purposes), and get this result:
I do not think that (...) .
Which basically means, the speaker does not agree with whichever thought he/she has. We can also replace that word "think" with some synonyms, and the sentence would still mean the same thing. Some examples:
I don’t believe that he will come tomorrow.
I don’t agree that he will come tomorrow.