In a dc sputtering system only the cathode is bombarded by positive ions. However, in a two-electrode rf sputtering system, both electrodes are bombarded. How come this bombarding substrate with positive ions does not disrupt the growing film?
Indeed that both electrode will be sputterred. However, the electric field that is applied to the electrode surface is different. I am not quite sure about the exact relation of this but basically the larger the electrode area, the smaller the applied electric field, so that the energy of the ions that bombard the surface would be lower. Usually in a RF sputtering system, the target will be one electrode while the sample connected with the whole chamber served as the counter electrode, so that the sputtering effect to the sample surface is minimized.
Better grab a book about sputtering, there it is usually explained quantitatively.