The examples given in the article are bad examples - any decent concept of utility could deal with them pretty easily - but there are good examples he could've used that really do show some underlying ambiguity in the concept around the edges. I think most of those are solveable with enough creativity and enough willingness not to go "Oh, look, something that appears to be a minor surface-level problem, let's immediately give up and throw out the whole edifice!".

But that sort of thing doesn't really matter as regards whether we should use utility for moral judgments. It doesn't have to be perfect, it just has to be good enough. It doesn't take any kind of complicated distinction between hedonism and preference to solve the trolley problem, it just takes the understanding that five lives are, all things being equal, more important than four lives.

This sort of thing is one reason I've tried to stop using the word "utilitarianism" and started using the word "consequentialism". It doesn't set off the same defenses as "utility", and if people agree to judge actions by how well they turn out general human preference similarity can probably make them agree on the best action even without complete agreement on a rigorous definition of "well".