Or if you deal in it every day, saying sequel comes more natural than saying ess cue ell. There's a lot more legitimately confusing things in the world of IT than pronunciation of commonly used names.

I don't fight my colleagues when they say "Suss" rather than the correct pronunciation of Suse Linux, because when it comes down to it, language is just an agreement that certain sounds mean something to the group that they are being spoken to. There's nothing inherent about the sanctity of language. If you can't be flexible, you might not be cut out for it.