I'm pretty sure I've seen "uber" (with either spelling but pronounced in English) on the web and on IRC as early as the 1990s. It likely spread beyond the online use when the web became mainstream.
Disclaimer: German native speaker who used to spend way too much time around linguists.
And you can't mention the German "super" in 2014 without pointing out this viral marketing campaign: https://www.youtube.com/watch?v=jxVcgDMBU94 (explanation: http://www.slate.com/blogs/browbeat/2014/02/24/supergeil_ede... )
I mean, you wouldn't catch anyone on German television pronounce Zuckerberg's name as /ʦʊkɐbɛɐk/, even if it may be of German (Jewish, I presume?) origin.
PS: I think the Duden and Wiktionary are full of shit -- I've never heard anyone in Germany pronounce "Berg" with an actual "r". Maybe I'm missing some subtleties of German phonetic transcription here, but that's an /ɛɐ/ diphthong if I've ever seen one.
Just.. don't. Occasional German references in English contexts are usually cringeworthy. Uber is ridiculous from this particular point of view, just because their name is absolutely useless. Unless you're trying to make the xth Nazi reference and think that German sounding bull.,.. might so the trick, please reconsider. The shop in this article at least knew then spelling and had a decent explanation. The other (HN loved) company is just... sad. I would suport the real über if they offer a way. Uber? Ridiculous, even before this article. But hey, who cares about the language you steal your laughable name from, right?