Why difficult to separate? Rythm goes straight to the body, harmony to the soul, if you like. You can have harmoneous and unharmoneous rythm and rhythmic as well as unrythmic harmony. For me both are important and the interplay between those two musically essential factors in all its shadings is essential to the musical experience. Therefore, if you take the impact of a given composition as a whole, you are right of course, it is like killing and disecting something beautiful, if you want to separate both factors, but that's what you do, when you start analysing a given piece of music.
