Yes, it can work. Assigning MIDI stop controls to some sampleset stops has no effect on the other stops.
Note the caveat in the user guide about trying to use both the stop controls and the pistons/toe studs on your digital organ to control Hauptwerk stops and combinations at the same time. You really need to choose one or the other, because the digital organ's combination system will fight Hauptwerk over stop states.
I've found pistons much more useful than stop controls, especially if I have to poke some of them on the screen.