So the indignation was a day late and a dollar short? Not surprising. Or perhaps they objected to the "mecca" part? Wonder how many Christians would have murdered people if it had been called Apple Heaven or Apple Paradise? Perhaps we should be insulted by Islamic phrases infiltrating the English language.
Approximately zero. There's also "My Blue Heaven," an oldie but goodie and, as a Christian, I've never fallen into a murderous rage on hearing it. Lots of phrases in our language refer to heaven or paradise in one way or another: "little piece of heaven," "God's country," "seems like paradise," etc, and you don't hear of Christians going on a murderous and destructive rampage when these phrases are used.
A better analogy would be if it had been called "Apple Vatican" or "Apple Canterbury" or "Apple Jerusalem." The word "mecca" (with a lowercase 'm') is pretty well ensconced in English as a term for someplace people make pilgrimages.
It was a natural for the site holiest (after Cupertino, I guess) to the Cult of Mac. As far as I know, Apple never used that as a code name for the store; that was the contribution of the blogosphere.