I think this deserves a better response.
I remain convinced that Thucydides remained siding with the Athenians, even after his exile. I have a few reasons.
First, the question of why he even wrote the history in the first place. He starts the book by saying that he started writing it when the war broke out (not after, as you said before), because he believed it would be greater than any war before it. Not because he thought the Athenian empire had gone too far, and not because the Spartans (or the colonies) deserved better treatment. Now much ink has been spilled about why the war (specifically Corcyra) happened, and whether it could have been prevented, but even if he were asking that question, that's again different from saying the Athenians went too far.
Second, while it is true that the Melian Dialogue is the only dialogue, it is not the only place where grand speeches are made. In fact, you could consider the Corcyra drama (between Athens, Sparta, and Cocrya) a dialogue of sorts, it's just not presented that way. So while it is true that he changed the format of delivery for the Dialogue, I don't think it's reasonable to assume he offered it more importance, and thus sided with Melos.
Third, the work is not only unfinished, but it ends mid-sentence. To carry through until the actual end of the war (404 BC), you need to pick up Xenophon. We have no way of knowing if there would be another dialogue, or if Thucydides would come out explicitly taking a side one way or another.
Finally, if you want to argue that he'd say the Athenian empire was dangerous, I'd need a good reason as to why. Consider how it came into being, as a result of the Persian war. Most of the colonies were quite happy with Athens protecting them from Xerxes, and it wasn't until Athens moved the treasury away from Delos that things got bad. And consider all the great things that came out of Athens: greek theatre, philosophy, mathematics, etc. Sparta offered none of this. In fact, most of the things we know about Sparta come from Athenian sources.
Therefore, I don't think it's too much of a stretch to say that Thucydides generally sided with Athens, and if anything, his issues were not with the empire, but with people like Cleon and Alcibiades, who (I imagine) he'd argue were not deserving of their titles, and dragged the wonderful empire into ruin.
However, I have not read the piece by P.J. Rhodes, so I will check that out.