It depends.
The fact that your dude tells you that he takes her opinion with a grain of salt means that he realizes that she's being a hater...especially given that you two have never met. Men, we can see through non-sense even if we chose to ignore it at times.
The chances that he'll start believing her one day are probably slim, but I can completely understand why you'd be annoyed by her insistence. What you can do is ask him to please either a) stop telling you that she's talking sh*t about you, or b) let her know that its not cool and that she needs to cut it out.
But I wouldn't worry that he'll believe her.
I have seen it go either way. Sometimes a guy doesn't want to date someone that his friends dislike while other guys couldn't care less. But this is a girl trash talking the OP to her boy friend and I think that makes a difference. If his bros trash talk his girl he might care more than when female friends do.