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The general problem with it is that it can be used too easily as an excuse. Hm, I think we should try to find the meta of this, this looks useful. Basically imagine a graph where various human situations are on the X and the usefulness of a given thing in that situation is the Y. And another graph, where the usefulness of that thing as an excuse is on Y. And if the second tends to be higher, that is not a good thing.
Another meta: there is a difference between thinking I figure X is good and thinking I am entitled to decide whether X is good.
For example the good old trolley problem. Pushing the fat man is the almost obviously right choice looking at that situation only ("shut up and multiply", feelings like OMG I am a murderer now do not matter as much as lives), but it is highly dangerous if people feel like they are entitled to take such choices, they are entitled to sacrifice someone without their consent for the greater good. This is a very different thing. It generates an excuse for others in far different situations.
A truly saintly person would push the fat man then demand to be punished, because the choice was right but he was not entitled to make such a choice and others should not feel entitled to either.
Pushing the fat man is the wrong choice because it forces fat men everywhere to constantly be on the lookout for consequentialists, and causes moral hazard by encouraging lax safety around railroads. Consequentialism is only indisputably the correct morality when everybody is perfectly rational and everybody has the same goals. In reality people have differing terminal goals and perfect rationality is impossible because of limited computational ability. Deontology is superior because it is far more predictable. Nobody has to waste brain cycles on avoiding being a convenient victim for some dubious "greater good".