C:\ProgramData is a standard Windows directory, and unfortunately we didn't make the game configurable enough to look in a different location.
There are ways to move your ProgramData folder, but do so at your own risk.
I'm not sure how safe it is to replace the sounds with half-second files. It will make your cutscenes fly by, since those are timed by the sound files. It could also increase CPU and hard drive usage, since the game will have to load a new sound file more often.
This situation will get better in Hegemony Rome, since we'd updated to sound engine to support reading from ogg files directly, but unfortunately it remains a limitation in Hegemony Gold.