I get the impression he wanted it stopped because he was disillusioned, and figured it just might work. Or it might not.

Concur. 'Damage done' was the Op's excuse to walk away from something he didn't want a part of anymore.

I can readily see the Miranda thing being as big a deal as it's made out to be too. Easily enough to trigger a new war. First, things can't be as stable as all that, seeing as how the old war hasn't even been over for a decade. Second, Killing a planetful of folk in an effort to drug them docile is in fact a pretty scary thing, and fairly recent too. Thirdly, and mostly: Dude. Reavers. The rim lives in utter, pants soiling terror of these guys, the government claims they don't even exist when they're responsible for their creation even? If I were a retired browncoat, I'd be thinking 'See? Here's exactly why I thought unification was a bad idea.' Shortly thereafter, I'd be calling my war buddies and rambo-ing up.

he didn't want the doctor to know the big scandal River knew.

Since he killed the doctor scant minutes later, I don't think it was a strong motivation.

I don't believe it's a real ending because The Operative said it mightn't be. Joss has left himself plenty of wiggle room.

The Operative himself told the Alliance that River Tam was no longer a threat. The fact that this gets mentioned at the end of the film suggests they're going to let her go. Sure, it's possible they won't, and that a potential sequel will include more we're-coming-for-you action, but it's also possible that they crew's been given an out.

Besides, we've got a new story issue to springboard the next film, provided they use it: How is Serenity going to find work now that all (or at least most) of the people who harbored her at any time have been killed by the Alliance? Mal and his crew have been made an example of, and I'm willing to bet they'll start the next story with more enemies, and brand-new ones.

Since he killed the doctor scant minutes later, I don't think it was a strong motivation.

Fair enough, I forgot that. Though he himself may not have known.

The Operative himself also told Mal he wasn't sure the Alliance would listen, Mr. Broom. Why give that so little weight in comparison?

Bon - he mightn't have known, but I can see no reason Mal would know more than The Operative.

The Operative himself told the Alliance that River Tam was no longer a threat. The fact that this gets mentioned at the end of the film suggests they're going to let her go. Sure, it's possible they won't, and that a potential sequel will include more we're-coming-for-you action, but it's also possible that they crew's been given an out.

I think it depends on where the next installment will be. If we go back to TV, we're likely to go back to smaller scale, stealing food to put money in the bank, then smuggling mud to put food on the table sorts of things. If it's another feature, then it'll be another big epicy type thing. Independants Strike Back is my guess. Civil war could be good.

Though he himself may not have known.

I thought he specifically didn't want to know.

While Miranda may have been the biggest of the secrets (or may not have), I don't think the Operative or anyone else knew for sure that she knew about it until later - the danger was that there was a host of things she might have known.

But this fits with the ending - they got the Miranda story out, sure, but it was the Operative's statement that she was "no longer a threat" that will (for the timebeing, or whatev) get the Alliance off their backs. The Miranda story being out doesn't matter, except possibly in the sense that they got bigger things to worry about right now - it's the threat assessment, which might easily be taken as meaning that she's dead.

There's no reason that the Alliance still wanting River means II would have to be about her. It just keeps them out of the light, still on the fringes.

The Operative himself also told Mal he wasn't sure the Alliance would listen, Mr. Broom. Why give that so little weight in comparison?

For entirely deus ex reasons--they've already done that story. If they're still hunting for River, I'm thinking it'll be in more of a taken-as-read fashion, like in "Safe" or "The Train Job," where it may be mentioned but not be nearly the strongest plot thread. Having them hunt her all over again makes it feel like a TV series on film, which is clearly not the feel they're going for.

See my post above.