Better would be a GUI=0/1 option to the bitcoin-qt.pro until a nicer (ideally
automake/autoconf) system is implemented...
Are you sure you want to require qmake for the daemon build?
I agree having a unified build system would be nice, but qmake doesn't add anything for non-qt software. Better to stick with a makefile.
If the goal is 'making it easier for the user' maybe it'd be best to make a bash script that wraps both, that builds the daemon if possible, and the UI if possible, and converts command line flags.