Yes, manual sensor clean locks up the mirror and shutter until you turn off the camera. Hold the camera facing down when you do this and use the rocket blower from below do any dust falls out.
The only thing that can go wrong it that you put the end of the blower too close to the sensor and then bash it into the sensor as you squeeze it. Yes, I actually did this with my T1i - left a 'gunk' mark, but actually no scratch. Still it was a heart-stopping moment and not one I recommend. Just don't jam the end of the blower into the mirror box, you don't need to get it close to the sensor, more like just getting dust out of the mirror box area.
In any case I think you will find the blower very useful, even if you don't use it on your sensor (I would give the 'sensor' a few blasts every once in a while though).