If you delete the DTMF tones from the sender's side (phone A), they will not get to phone B! They must go through the voice channel to be able to use them from the other side.
If you're worried that your DTMF tracks will be listened to and decoded on a public phone, your problem is valid. There is no way to protect yourself here. Do not use public phones!
However, on the call center side, they use DTMF masking. They detect the DTMF tones beforehand, process them first, then convert them all into a flat tone so that they can not be decoded by a person from the organization.