The earth bonding is there to protect the dwelling occupants from an electrical shock. If there was an existing electrical problem where the pipework was becoming live you would already know about it, either by an RCD tripping, or an MCB or fuse tripping. Im not saying by removing the bonding from pipe you wont suddenly and all be it untimely have a system fault, so if the bonding can be kept connected to the pipework during undertaking of the work you should be good.