Uhh wait..I don't get the problem here. You could just not do anything else
other than your audio work and still use the alsa jack plug. Then change
every app's output to jack; those that can't will output fine via the plug.
I don't know about other DEs but in KDE nothing disturbs me as long as I
don't run anything non-proaudio. If you don't use a DE then the more reason
to not fear anything.