1. Like the nations of the Earth are going to just drop the Cold War and start working together to stop the extraterrestrial threat? Un-fucking-likely, sez I. Even if you could convince every nation that it's not just some crazy trick the US is pulling, or something like that, and you could convince them the best way to deal with the threat is to create a peaceful world alliance, it'd take some serious diplomacy to get such an alliance together and coordinated.

   I agree with Steven here:  This is the weakest part of Watchmen for me as well.  But we have the benefit of post-9/11 events to aid our analysis.  September 11th showed us that just because other nations may be sympathetic toward the U.S. in times of tragedy doesn't mean those nations will abandon their own interests or aspirations, or trust us in all matters (or that the U.S. will act any more multilaterally).  And there will probably always be some fringe elements who would suspect the U.S. of perpetrating any horrific act on its own citizens.  Looking at the events in Watchmen, it seems plausible that the USSR might be so shocked by the horror that befell New York that they would withdraw their troops from Afghanistan out of sympathy.  (I can also see how a nation might use such an opportunity to press its advantage against an opponent.  Which outcome is more probable is anyone's guess but probably depends on knowing much more about the situation at hand).  But it does seem unlikely that one isolated event (no matter how horrific) would suddenly cause two nations with long-standing conflicts to become best friends forever.  In Moore's defense, however, I'm not sure just how long-term he intended us to view the peace on display at the book's end.  For one thing, the threat of Rorschach's journal being discovered is the final scene in the book–the implication being that Veidt's plan will be exposed after all.  Even if we discount this (as most people living in the Watchmen-world probably would were it ever published), I don't know if anything in the story requires us to assume that Moore saw this plan as viable.  Although we see signs of what appears to be a peaceful, Russian-influenced U.S. in the last few pages (a "Burgers 'n' Borscht" fast-food joint; a sign advertising a screening of Tarkovsky's The Sacrifice (another nice thematic touch by Moore); a "One World, One Accord" poster), for all we know, these may be isolated occurrences, and may all be attempts by Veidt to manipulate the public (like the "Millennium" billboard also on display, replacing the now-retired "Nostalgia" campaign).  And even though Veidt says he now wants to "help [Earth] toward Utopia," there's no guarantee that he'll be successful in his efforts.  Consider the example Veidt offers to demonstrate the brilliant "lateral thinking" of his idol, Alexander of Macedonia:  Alexander didn't succeed in untying the Gordian knot; he only succeeded in destroying the problem.  If the point of the Gordian knot was to untie it, Alexander was a failure, not a success.  Similarly, although Veidt may have eliminated the immediate problem facing him (the US-USSR tensions in Afghanistan), he didn't learn anything about "untying the knot" (establishing lasting peace).
   

2. And by the time it's coordinated, somebody's going to have figured out Veidt was behind it all along, and that's the end of the alliance. If crazy fuck Rorschach managed to figure everything out, the CIA and the KGB and whatever other intelligence organizations are going to have it figured out it about 5 minutes.

   Perhaps, but Rorschach is also somewhat of an...unconventional thinker, so maybe not.
   

Although most of the "superheroes" are less than perfectly heroic, I still think Moore depicts them as trying to do good/right.  Or at least most of the human ones–Dr. Manhattan seems too far removed from humanity to be considered heroic, and the Comedian seems too amoral.  Even Ozymandias acts in a manner motivated by what he considers to be right (viewed from a utilitarian perspective).  Further, the scene where Malcolm (the psychiatrist who treated Rorschach) attempts to intervene in the fight between two women always struck me as heroic/uplifting.  Although his faith in an objective moral order and higher meaning has been shaken, and although his estranged wife begs (orders) him not to get involved, Malcolm soldiers on:  "Gloria, please.  I have to.  In a world like this... I mean, it's all we can do, try to help each other.  It's all that means anything."  Although the worldview in Watchmen might appear cracked, I don't think it's broken beyond all hope.

Well, Dr. Manhattan was already depicted as a cold-blooded killer earlier in the book (in chapter four he's shown blowing up a villain's head and the narrative caption reads "The morality of my activities escapes me.")  Plus, Jon cheats on Janey with the younger Laurie, so it's not as though his motivations were traditionally moral.  In fact, throughout the story, Jon only seems to respond to logical considerations, not moral ones.  As for why he killed Rorschach rather than somehow else incapacitating him, perhaps it was because Manhattan still viewed human life in the abstract:  Although he had come to admire life as "the thermodynamic miracle," there was no indication that particular human lives meant very much to him.  He had already grown distant from Laurie (his relationships–like his clothing–seemed to be artifacts that he shed along with his humanity).  Perhaps Moore had Manhattan kill Rorschach to drive home the point that Manhattan–with the power to create life as well as destroy it–had become more god than man.