The reason why holy wars pop up is given in the first sentence of your writing. It's because people tend to be polarized - black and white, right and wrong. Real engineers recognize that there is usually more than one way to solve a problem. Complex problems almost always have varied solutions, each with their own advantages and disadvantages.
I suspect holy wars pop up in the computer industry due to the younger age (actually, less experience, age is only related to this) of the people involved. They haven't had enough experience to know that there is more than one way to do something. Programmers are especially guilty of this - they find a way to do something and they keep doing it that one way. Microsoft, despite radical advances in hardware, continues to write its OS' the same way. I truly feel sorry for them, because when computers become massively parallel and distributed, Microsoft will not have the skills to adapt.
In a larger sense, holy wars have more to do with ego than anything else. Computer geeks seemingly have inexhaustible ego sizes and pride themselves on it. When it gets down to it however, they are insecure in their knowledge - the field is so vast that someone, somewhere, knows more than they do and it bugs them. Not everyone, but alot of us do this. This industry is very young, and new things are happening all the time. The idea that I might not be up to date on something does worry me sometimes. Do I know as much about hardware as the 14 year olds out there right now? Maybe. That bothers me alittle.
Wait for the industry to mature alittle more, and these holy wars will decrease both in duration and intensity. We'll never be rid of them, of course. Besides, sometimes we need a good holy war to get to the heart of the matter - "Richard Stallman v. Hillary Rosen: Steel Cage Match!" I'd like to buy a ticket, please.
Society needs therapy. It's having
trouble accepting itself.