Music theory is a sub-domain of musicology focusing on the science of music often handled within the context of time or periods of time. So doesn't the science of music touch all physical attributes of music? And if it doesn't wouldn't it be incomplete science? And aren't those physical attributes constant across all styles? The only difference being how periods and styles limit the utilization of the science of music.
Is it reasonable to mix the history of music (an ever changing dynamic), with the science of music (a constant); and call them the same; "music theory"?
I think so. Because music theory is just a view, perspective, or model of music within some context. But if you don't have a some well formed view of music you're fishing without bait.
You present interesting points. Music is ever changing, but the "science" of music is pretty constant in most cases... Kinda like Dazed and Confused... I keep getting older, but high school girls stay the same.. (sorry... had to xD)
Anyways, music theory is based on what we have designated as our musical setup. If you look at a piano, we have sharps/flats and whole tones. There is a sharp/flat between each note except BC and EF. Why? I think it was partly due to making the piano an instrument that can actually be manipulated. If there was a black key between every white key.. how would anyone know where middle C is located?
Also, we have A and A# and they are noted and understood by certain amount of vibrations/ cycles per second. We understand that A(4?) is 440 cps, it really seems arbitrary. Why not 445 vibrations as A? Why do we need to tune to these certain vibrations? Why not invent a new tuning system and have 442 vibrations be called Alpha Ding Dong?
Music theory, of the western culture, is based on the idea that our notes are to be remained constant in all ranges of all instruments. A4 will be A4 on any instrument.
So yeah. Its reasonable to mix theory with history, but maybe more so that history is mixed into theory.

Are we really that angry now?