gtranquilla, you're talking about a few different things at once.
First, if the vibration is so intense that it is over the measurement limits of the sensor, you're done. There's no need to talk about a filter, etc.... it's going to crash, period. That's a whole other problem.
So, you mention the Kalman Filter. Yes, the Kalman Filter should be exposed to full-rate accelerometer data. It is an integrating filter, which means it naturally averages out any vibrations. (assuming it's been programmed correctly!). But the angular rate controllers need filters to get rid of noise. We actually had a fascinating situation just last week. A user was experiencing horrible vibration, that he just could not get rid of. It was at a specific frequency. He didn't want to go to the 10Hz LPF option, because he felt that made it less stable. I use 10Hz all the time on helis, though they are naturally stable. Anyway, one of the other devs thought that what he was seeing is "structural vibration", meaning that the control loop was actually exciting his airframe's natural frequency. The prop was getting control inputs at whatever Hz the frame resonates at (I think it was around 30hz). So the guy hacked in a notch-filter at the resonant frequency (beauty of open source...) and the problem was solved.
Cool stuff, and it reinforces what I'm saying about the response rate of these machines.