Read the Wikipedia page on the Compact Muon Solenoid. There were some significant computational challenges involved, including how to (pre)process and store terabytes of data per second. These are challenges that push the envelope at every layer of computing, from hardware to the OS and application levels. It's not an informed proposition to say that the OS was some replaceable commodity with an unimportant role -- that's like saying Linux is unimportant at Google or Amazon. The ability to tune the kernel wad definitely crucial.

I would also question whether 20+ years of devlopment on a private UNIX clone would have produced a better result than Linux. There are plenty of private UNIXes but sarcely a convincing argument that a single one is better than Linux in some meaningful way.