Anyway, I think that Quetzalcoatl would be definitely perfect if the chorus was sung in Quechua or any other Mayan language instead Spanish.

Two relatively minor things concerning your post:
Quechua is the language of the Incas not the one of the Mayans (which speak... Mayan by the way). And given that Quetzalcoatl is the way the Aztecs named that god (the Mayans called him Kukulkhan), you should ask that that song should be sung in Nauatl (the Aztecs language). ... (just a stupid historical remark, that's all

)
The second point is a question that Christofer raised somewhere in an interview about this very same subject: Why people always complain about the parts in Spanish and never about the parts in English? ... I mean, at least there is a historical conection between Spanish and Nauatl.
What is the relation between English and Nauatl? .... weeell

.
Anyway, personally, I have never really cared in which language that song is sung (that song is not even one my faves anyway). The only thing I really care about is the fact that Christofer and Thomas decided to use that legend to make a song, which is pretty cool of course!.
Yeah, I commited a mistake... But you got the point, and that's what counts

As blackrose said, English is a neutral language. Plus, using ALWAYS exotic languages would make the songs kind of unacessible. I just think that it looks a bit cruel to use the language of who destroyed their civilization (Not an accusation. I'm not blaming the band, or something like that - I know very well that wasn't their intention. It was just an impression I had).
Also, using Nahuatl (Yes, not Quechua

) would look much more "Therion", in my opinion.