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I would object to calling these "devastating counter-examples", they're more like unsolved problems. It seems overly dramatic. I'm not a perfect Bayesian agent, I use my intuitions a lot, but that is not grounds on which to reject Bayesianism, and I think we could say something similar about consequentialism. I may not know how to perfectly measure relative happiness, or perfectly predict the future, but it doesn't seem like that should be grounds to reject consequentialism entirely, in favor of alternatives which don't cope with those issues either.
One very common error people make is to treat "utilitarianism" and "consequentialism" as if they were one and the same thing. Utilitarianism makes claims about what is moral and what is not. Consequentialism makes claims about what sort of properties a moral criterion should have. Criticisms about utilitarianism, therefore, are often taken also as criticisms of consequentialism, when in fact the two are distinct concepts!