There will definitely be phonemes shared by both, of course, due to the mechanics of the human mouth and throat. Not sure why you feel you couldn't use 'Sunrie' as a term. People have certainly made up terms before.
As for the rest, eh. Player fiction and later contradictions are an old chestnut. I personally tend to be wary of filling out big important concepts and pieces of the setting. Other people differ, and I presume they either have plans for later reconciliation or don't think they will be contradicted.
Well I can't use blue because you said.
Now Sunrie, of course...it's my friend's term ... although if I recall his character's story (remember this was OLD-school free-form forum and chat RP -- Red Dragon Inn & Chatalyst if any of you guys remember those from a decade or so ago) was that the Sunrie were a race of immortals.
Anyways, I'm just using that as an example of a completely made-up title that has no "real-world" connection or connotation.
I see the argument about "well, it's not REALLY Latin/Sanskrit, but represents that sort of culture/language," though being honest, since it IS humanity we're talking about, merely "a long time ahead, in a galaxy far, far away," there is a def tendency to take that sort of thing at "face value".
Also, the "EVE takes place 2k years from now, our cultures, languages, etc, would be COMPLETELY unrecognizeable to them," thing.... really, humanity hasn't changed a whole lot in the past 2000 years. The toys have gotten better. We've procreated a lot more, and concurrently created weapons capable of removing infinitely more lives from the world in a single shot....but the same archetypes, the same biases, the same basic sociological and geopolitical factors are still easily found. To me, the politico-social landscape of EVE (complete with Goons, the ILF, etc) is very believable. The same types reigned 2000 years ago, they're still around today, and should humanity actually survive that long, there's every reason to believe there'll be a Mittens, a Bataav, and probably also some dude who does "clever" plays on words in other languages to bring about tawdry semi-hilarity as well. ;-) (hai!)