I want to stop my dogs antibiotics can that cause harm?

Yes it can. Antibiotics must be taken for the specified amount OR titrated down to off, otherwise the infection can come back a lot worse than it originally was. I'd talk to your vet again and tell him your concerns. There are plenty of other antibiotics out there that he should be able to switch to another one depending on the strain of bacteria. But don't just abruptly stop them because that could cause a lot more problems for your dog.