If your algorithm accounts for future states - and it'll have to, to be practical - "assigning minimal resources to the really unhappy people to let them die from neglect" is also part of the set of options.
I have met at least one vegetarian (who is also a utilitarian) who has said that many species of animals currently suffer so much that it would be better if those species were all dead. I've heard of others who share this opinion. I call it the "Final Solution" to animal welfare; I think the name is quite appropriate.
Anyway, well, then, that seems to leave some big question marks. How is everyone who goes through utilitarian moral reasoning supposed to decide between help and neglect, and hope to come up with the same answer? (Because if two people come up with sufficiently different answers, it may lead to one or both concluding that the expected utility of violently enforcing obedience from the other person is worth the cost, unless they have deontological rules of some sort. Like the kind that the article says Mill supported.)
I don't think that's quite as marginal of an opinion as you think.
If someone is vegetarian/vegan for ethical reasons, it's because they want there to be fewer factory farms. This would of course mean that the animals they would have eaten wouldn't exist at all, so of course they'd consider nonexistence better than a life of torture.
"I'd rather you not have lived at all, rather than live a life of torture" is a pretty mainstream opinion in general, I think.
Possibly. But extinction of the species completely eradicates hope; I would prefer "life under torture with a chance of eventually obtaining a good life" over "permanent nonexistence".
Unless cloning counts? Is extinction okay as long as we have some copies of their DNA and plan to clone them into a decent life eventually? I feel rather uneasy about that resolution; at the very least I'd want to see a species successfully reconstructed in this manner before giving the possibility moral weight.
