Can you please elaborate what you mean by this? Thucydides, being a native Athenian, obvious fought on the side of the Delian League/Athenian Empire; that isn't so much a choice as a natural course of action, the allegiance to your family/polis being a central part of the identity of the Hellenes. His history of the war was written after he went into exile, and written in a largely neutral way. In fact Thucydides went out of his way to paint certain Athenians, such as Cleon in a very negative light, and was very positive on certain Spartan generals such as Brasidas.
The placing of the Melian Dialogue is particularly interesting not just because it's the only dialogue in the whole work, but because it was immediately before the end of the book, and the following book deals exclusively with the disastrous Sicilian expedition of Athens. Readers going through the work in order would read about the arrogance of the Athenian delegates in the dialogue, directly before reading the absolute misery of the Athenians sent on the Sicilian expedition where they were eventually completely destroyed. It's easy to get the impression that the Athenians have been hoisted by their own petard, and it seems reasonable that is precisely what Thucydides the historian want us to take away from it. Not that the expedition was depicted without sympathy to the Athenian soldiers, the two battles of the Great Harbour of Syracuse contains some of the most gut wrenching scenes of battle ever written in a history, and it's painful to read even now because of the masterful way Thucydides records the despair that have taken over the Athenians by the end of the second battle when their fate was sealed.
Given this larger context, I don't think it is reasonable to say Thucydides "sides with the Athenians" in the Melian Dialogue. It is true he did not record his own moral judgement on the events in the work, but the structure of the history suggests that he certainly did not support what Athens did to Melos.