It strikes me that the controversy about Klingon has more to do with its fictional origins than number of users. Is this not true?
I don't think so. We will certainly encode Tengwar and Cirth, which have corpora of documents in them. Klingonists universally prefer Latin, and it was the judgement of the UTC that the usage criteria hadn't been met.
And of course, there's all that discussion on Tolkien languages online... all of which used Latin transliteration (with slightly varying standards too: accented vowels, doubled vowels, tripled sometimes, etc etc. "More than one orthography"). This gets back to "everything's a code of Latin" again.
~mark
P.S. Make no mistake. To the extent that there are "degrees" of this, while I think Klingon should get encoded, I certainly think tengwar and cirth et al deserve to be encoded "more" than Klingon does.