No filter media or a sponge will not kill the bacteria within your liverock. However, the bacteria in your live rock takes nitrates and further breaks it down to harmless nitrogen gas. Bacteria within a sponge or pad can not do this but it will be very efficient in making nitrates.
Live rock can only convert nitrates which are produced in it's vicinity into nitrogen gas so the nitrates that are produced by your sponge will enter the water column and you'll start to see your nitrate level rise over time.
Many people use sponges or pads as a pre filter to help polish the water a bit. This is fine, but they have to be washed very frequently to prevent a buildup of nitrate producing bacteria.