I'd like to hear your interpretation, then.
Okay...
My take on it is that the Amarrian Empire has a language, and that language is Amarish.
[1]Amarrian Scripture has accumulated over the millennia. "[M]any of the earliest books of Scripture appear to have been written directly by the founding prophet"
Dano Gheinok who preached
over 15,000 years ago, around the time when the EVE gate closed and the EVE civilisations collapsed. I think it's those very old portions of Scripture that "hearken back to the very origins of Amarr society, written in a tongue so ancient as to be unreadable by today's Amarrians": most likely the ancient ancestor of modern Amarish.
[2] I don't think that all Scripture is written in "Ancient Amarish": I think Scripture is written in whatever version of the language is current when it's written.
The other half of that quotation is: "[t]he collective writings have been maintained and updated throughout the centuries by Imperial Theologians".
[3] It's up for discussion how much of that maintenance and updating is selection of texts for inclusion and study, and how much is updating the language of older texts so they communicate their messages correctly. If we assume that the
Book of Gheinok is even vaguely contemporary with Dano Gheinok 15,000 years ago it would be one of those ancient-language texts, and yet we have it and use it in a translation that seems to be intelligible even to those without capsuleer translation implants.
I think people in the Khanid kingdom most likely speak Amarish.
The people known as Khanid were "[a]mong the oldest of the bloodlines to be assimilated by the Amarr". According to the histories they were contentedly, and in some cases zealously, part of the Amarrian Empire for around 3000 years. "A large Khanid population" lives in territories which were not part of House Khanid's demesne when Khanid II seceded, and have remained with the Empire. "Today, a large Khanid population remains in Amarr, loyal to the faith and royalty of the Empire. Many of them yearn for the day when the two kingdoms will reunite." To me, a group that was "assimilated" 3000 years ago and distributed through a wider empire most likely speaks the language of that empire.
[4]I think the peaceful missionary approach to conversion is relatively new for Amarr (and possibly not something they're good at yet).
Before encountering the Federation, around 167 years ago, I think Amarr had conquered every culture it encountered.
[5] It was sort of "what Amarr did", bringing truth, justice and the Amarrian way, using the sword and the laser. My sense is that they're now exploring the idea of converting people with words rather than with force, but that the idea of making religious instruction manuals in other languages is novel, and possibly seen as a stepping stone to the Real Thing in Amarish. That's just my feel for it, though.
Also, the fact that Amarrish is the official language of the Empire doesn't mean that there aren't other languages spoken. As Odelya pointed out, in the history of human empires it was rather the rule that they were multi-lingual. The Persian Empires, the Roman Empire, the Empire of Alexander the Great, the Ottoman Empire, the British Empire, the Holy Roman Empire, ... actually, I can't think of a single Empire in the history of humankind where all languages but one were eliminated.
Of course the Amarr would insist that their language will be installed as lingua franca regardless of whether there are also other languages spoken within the Empire.
At this point I think we're each asserting our preferences. I think the language of daily life and religion in the Amarrian Empire is most likely to have superseded whatever might have been there beforehand among the people-we-now-call-Khanid who were--note the choice of words--"assimilated" into the Amarrian Empire around 3000 years ago. It sounds like you don't.
We could argue about things like Romance languages and the differences between the areas where vulgar Latin did supplant the previous local language vs the places where it didn't. While that debate might be interesting in its own right
[6], I don't think it would tell us much about the Khanid. I've read the PF and I think--okay, I'm pretty sure--that Khanid speak Amarrian. You've read it and you think they speak something else. Only CCP can tell us for certain.
[1] "All the major races in EVE speak their own language [....] Amarish, the language of the largest empire [....]" http://community.eveonline.com/background/potw/default.asp?cid=apr02
[2] "Gheinok appears early in the Scriptures as a preacher and a prophet." http://wiki.eveonline.com/en/wiki/Dano_Gheinok#History
"While it appears that Dano Gheinok based much of his religious views off an established dogma, many of the earliest books of Scripture appear to have been written directly by him." http://wiki.eveonline.com/en/wiki/Dano_Gheinok#Religious_Influence
"8000 AD Dano Gheinok proclaims himself prophet and sets the foundations of the Amarr theocracy state to come" http://wiki.eveonline.com/en/wiki/Timeline (NB: Dano Gheinok may have had a long life, or one of the versions of the history might be reversed or retconned: the timeline mentions him 72 and 61 years before the collapse of the EVE gate, but his biographical entry describes him as "the first recorded leader of the Amarr people following the collapse of the EVE Gate". It's only 72 or 61 years difference, around 15,000 years ago, so let's shrug about natural long lifespans for Amarr and move on.)
[3] "The collective writings have been maintained and updated throughout the centuries by Imperial Theologians and include texts that hearken back to the very origins of Amarr society, written in a tongue so ancient as to be unreadable by today's Amarrians." http://wiki.eveonline.com/en/wiki/The_Scriptures
[4] "Among the oldest of the bloodlines to be assimilated by the Amarr, the Khanid people have endured the political turmoil of their leaders with great dignity and calm. Originally fellow settlers alongside the Amarr on the planet Athra — known today as Amarr Prime — the Khanid were swept up by the nation of Amarr and the powerful message of their faith during the height of the original Reclaiming. For centuries they were exalted members of Amarr society, until a bitter feud between the Empire and an Amarr heir representing the Khanid forced an outright secession of the bloodline's majority, and the subsequent creation of the independent Khanid Kingdom. Today, a large Khanid population remains in Amarr, loyal to the faith and royalty of the Empire. Many of them yearn for the day when the two kingdoms will reunite." http://wiki.eveonline.com/en/wiki/Khanid_%28bloodline%29
"AD 20078 The Reclaiming is launched. The Amarrians start a war to conquer all the lands on Athra [....]
AD 20544 The Amarrians conquer the last state on Athra. They now control the whole planet" http://wiki.eveonline.com/en/wiki/Timeline
Current date is around AD 23236 (YC 0) + YC 114 = AD 23350.
[5] http://wiki.eveonline.com/en/wiki/Timeline Fun tip: search in-page for "conquer".
[6]"A group (a state or an ethnicity) can spontaneously adopt a different culture due to its political relevance, or to its perceived superiority. The first is the case of the Latin language and culture, that were gradually adopted by most of the subjugated people." http://en.wikipedia.org/wiki/Cultural_assimilation#Cultural_influence