You didn’t actually read Watchmen at all if you think that’s the conclusion he “wanted” readers to come to. The final words of it are, “I leave it entirely in your hands.” Literally telling the reader to come to their own conclusions on what happens next, who was right, and what it all meant. The outcome Moore thought would be best and what other readers thought would be best and how they all differ is a feature, not a bug.
He doesn’t even “side” with Veidt. The guy’s Superhero persona is literally named after a poem about all a man’s accomplishments crumbling to dust in the wind. Suppose there might have been a reason Moore picked that name in particular for a character?
Moore may be more blunt in his disliking of Rorschach now, but he’s also the only person who’s really worth liking, and the character who’s mindset and psychology are dug into the most out of Watchmen’s cast. And while Rorschach is indeed a very sympathetic and pitiable character, he’s also heavily flawed. FFS, the dude brushes off his idol sexually assaulting someone as a “moral lapse” because Rorschach projects his need for a strong father figure onto people like The Comedian or President Truman.
Speaking of Truman, Rorschach spends a lot of his journal praising the guy, particularly for dropping the atomic bombs for the greater good. But when Ozymandias makes a big convoluted space squid and drops it on a city for the same reason, Rorschach very quickly changes his tune. When Rorschach’s own logic and morality plays out in front of him and in his city, he can’t stand it and changes his tune.
Now, Truman and Veidt’s actions and circumstances aren’t exactly the same, but the comparison between Ozy and Truman is about the public moral argument from the government that people like Rorshach believes, which is that is was a bad thing that had to be done to prevent even more bloodshed. In the much more intense Cold War of Watchmen, Ozy's logic is exactly the same as Truman's, he killed some to save a lot more. Circumstances are different but the moral argument is the same.
But for all of Rorschach’s flaws and hypocrisy, it just makes him and his actions all the more interesting to dissect compared to the other characters Watchmen follows.
Daniel is a superhero because birds and airplanes are neat. Laurie's there because her mom said so. Jon's there because of the government. Eddie wants to kill minorities for the epic win lolz. Rorschach's there because he has been the victim and no one helped him. It's why he does what he does even when there seems little point and the act is ultimately futile.
And that status as a victim is why he's the only one with the guts to tell Adrian to piss off. Jon, Dan, and Laurie can dismiss the deaths of millions in the name of the greater good, but Walter Kovacs can't, because he is those people.
Consider who dies in the blast. It's the Bernies. The lesbian couple. The shitty part of New York where Walter lives. Mrs. Sharip (who reminded Walter of his mother) and her children are very likely killed by Adrian's actions. These are people that Walter Kovacs saw every single day and now they're dismissed as suitable foundations for Adrian's plans.
And hey, once the Cold War is over and the Russians back off, what's the stop Veidt Industries from going global?
Walter is different from all the other characters because he's not a "hero". He's the victim. Being a working class, illegitimate abuse survivor in instrumental to his every action as Rorschach.
TL;DR: No, Moore didn’t side with Ozymandias or Rorschach, he just told a story and left it up to the readers on what it all meant.
