Watchmen is the Trolley Problem

So Rorschach is a deontologist (derives morals from pre determined rules regardless of what consequences they have, like Kant's categorical imperative) and rest all are consequentialists.

I too disagree with deontology in the sense that it assumes morals are valuable in themselves, without having to consider anything else. Which doesn't seem like common sense at all.

But I also disagree with consequentialists in that it's wrong to assume, especially when considering such large scale impacts, that it's possible to predict consequences. Ozymandius is being awfully presumptuous in thinking his plan could work. Dr Manhattan on the other hand, despite being an all knowing god or whatever he thinks of himself earlier, after learning of the Comedian and Silk Sceptres's stories, which he wouldn't have anticipated, gains some humility. Instead of writing them off as predictable (e.g. when two people die while he teleports a crowd away from a riot, he says more would have died had he not done so. Parallels to ozymandius teleporting the monster btw), Dr Manhattan gains appreciation for the unreliable/unpredictable human nature.
(Off-topic:
And this realization, I feel, parallels the throwing away of his father's watch. Just as his father states that relativity proves the predictable mechanical nature of his watches to be pointless, so does Manhattan discards his view of the humanity being predictable/mechanical.
But when the watch shatters on the ground, just as his body did in the science experiment, and humanity did because of ozymandius's monster, Manhattan is drawn back to reassembling it, to repair his father's watch, to reassemble his body, to make his own humankind in a distant galaxy.)

Ok, contrasting the deontologist with the consequentialist for a while-
It doesn't matter to a deontologist once the moral decision has been acted upon. It only matters before performing the act- whether the act is good or bad a priori. Once the deed is done, you're already good or bad whether or not things turn out alright or not.
Rorschach faces a crisis being a staunch deontologist and knowing the terrible truth which now he's obligated to disclose(just as he felt obligated to inform other superheroes about comedian's murder at the start). And he knows well that it'd be a very bad thing to do, but this gut feeling goes against all his principles, and he pleads for Manhattan to kill him as he can't bear this realization, like seeing his face in the mirror.
(Side note- the true face being that Rorschach was still the consequentialist Kovacs after all)

It doesn't matter to the consequentialist whatever deed was performed as long as the consequences turn out to be alright. No matter how many bad things you do, it doesn't matter as long as the ultimate consequences end up being better than the alternatives.
Ozymandius faces a crisis after the act. He knows he won't live long enough to see the consequences and has the gut feeling that what he did was really terrible. He seeks a consoling answer from an all knowing god. But Manhattan condemns ozymandius to his own philosophy- only consequences will tell whether what he did was right or wrong.

Relating this to the trolley problem.
If you are a consequentialist, the trolley problem decision is like begging the question. If you know fewer people will die in one of the routes with no side-consequences at all, then the answer is already in your hands, if you subscribe to consequentialism. It hinges on knowing the consequences; What if the track with fewer people has your family? What if some classical tragedy shenanigans are to happen after you chose killing fewer people, that end up killing more eventually? What if the track with more people had Hitler among them (statistically less improbable too if you think about it) Consequentialism fails to be useful because it assumes knowledge which is many a times not possible practically.

Deontology gets around this problem. May the track with fewer people have your family, may the track with more people have Hitler, if it's categorically wrong to kill a human, it's more wrong to decide to kill more humans and thus you kill your family to save the Hitler. You see how this is throwing the baby out with the bath water?