Obviously, the Melian Dialogue is an invention of Thucydides, but what ideas is he trying to get across? Does he think Melos should have bowed to necessity and submitted to Athens's ultimatum, and does he think the Athenian position was manifestly unjust? Melos became a byword for cruelty in the Greek world; does Thucydides comment on the aftermath, and whether or not Athens was pragmatically justified in crushing Melos?
There's a couple of things to keep in mind with Thucydides. One is that he was a disgraced Athenian strategos (general) who was banished for appropriating precious metals from silver mines in Thrace. As such, The Peloponnesian War is a result of his banishment, and in it he recounts some of his personal experiences and what he claims to have gathered in the course of his research travelling Greece during his banishment.
Another thing we need to keep in mind is that though he was banished by his compatriots, Thucydides was an out and out Athenian boy. In the course of his writings he idolises Pericles to the point where you'd believe the man could do no wrong (see his Funeral Oration in 2.34). One of the things about him is that because Thucydides hold himself up to the first standard of attempting neutrality in an effort to write largely unbiased history, he's still got a subtle pro-Athenian bent, even if he acknowledges its flaws. The tendency of historians after him hold him up as a gold standard, and as such it lulls people into a false sense of security regarding his biases. In late 20thC discourse on him we do start to see this questioning of his motives more closely, but that's another topic.
With that out of the way, let's start with addressing his dialogues.
It's hard to comment on what exactly Thucydides personally thought of the massacre. One of the main things Thucydides introduces to his audience is what we'd call realpolitik, the justification that social/moral conventions are just that, conventions, and that might will not necessarily make right, but it does steer the polis it towards geopolitical goals. This can be seen in the two main dialogues of The Peloponnesian War, the Melian dialogue and the Corcyraen debate, wherein personified representatives of various cities express their desires and attitudes. I don't think Thucydides takes a side in portraying the Athenian treatment of the Melians as particularly brutal because of brutal people. He depicts it as if Athens believes Athens has no choice, which the Melians point out that they do have a choice. Given that this is an explicit rhetorical device entirely invented by Thucydides as a means of expressing the political exchanges, he is the one who puts the words about choice into the mouths of the Athenians and the Melians. He also certainly acknowledges that the treatment of the Melians was particularly harsh.
About this same time the Melians again captured another part of the Athenian lines where there were only a few of the garrison on guard. As a result of this, another force came out afterwards from Athens under the command of Philocrates, the son of Demeas. Siege operations were now carried on vigorously and, as there was also some treachery from inside, the Melians surrendered unconditionally to the Athenians, who put to death all the men of military age whom they took, and sold the women and children as slaves. Melos itself they took over for themselves, sending out later a colony of 500 men.
5.116, Rex Warner's translation. (PDF warning)
To me the final lines about the Athenians aggressively colonising Melos after the all-but-genocide of the Melians underscores his understanding of the siege as an act of Athenian imperialism. He could have easily chosen to not include this note about its colonisation by the Athenians, but he does.
It's also worth noting that Xenophon (in Hellenica 2.2.3) writes that the slaughter of the Melians, like you note, was widespread knowledge, and that the Athenians feared that the Spartans would do unto them and they did to the Melians. (The Spartans didn't wind up doing this, but the Plague of Athens was just as bad according to Thucydides.) But this byword for cruelty was spread by word of mouth, and not explicitly as a result of The Peloponnesian War.
As such, there's no real way of knowing what Thucydides personally thought, but we can read into the text a little and come to some sort of conclusion. I hope this helps your question. Also thank /u/SilverRoyce for linking me to your question, I wouldn't have seen it otherwise.
Can I ask what brought this question to mind? I think you might mean a couple different things depending on the context of your question.