computers were the bottleneckPerhaps, but we were discussing software. Specifically, "Linux" vs "some other operating system".
I agree that advances in computing must surely have a lot to do with the discovery of the Higgs, but such advances are about hardware, not operating systems. Since the 1990s, billions of dollars, both public and private, have been spent to keep Moore's Law rolling forward, and that's most of what makes modern computers more capable.
Anyway, it occurs to me that this discussion is a classic bikeshed. Rather than debate tricky and obscure issues like the quantum mechanics behind the Higgs phenomenon, the engineering of supercolliders, the politics of getting supercolliders funded, the ins and outs of data processing algorithms at CERN, or the techniques of manufacturing transistors with a 20nm gate size, we have fallen back to debating whether or not the license used for the operating system was vitally important.
If CERN had had to implement a Unix entirely from scratch in order to do their job, they would have done so. It would have been a minor side issue. Indeed, from a certain point of view, that may be exactly what they did. Why discuss how Linux was vital for CERN's scientists, but not the other way around? Perhaps the reason why Linux was so good for high-energy physics is that high-energy physicists built it that way?