Why not cull her from the flock, she could still be sick, he would be able to tell better than you.

Frankly she is a pet as is my all of my little flock.

I would put her back in with the hens and take the roo out for 3-7 days. I would think if she was contagious that some of the other hens would already be sick.
Put the roo somewhere where he can't see the hens while they are seperated. Maybe this will change the behavior.
I never saw this behavior before between a hen and a roo that have been together. It sounds more like something two roos would do.
Maybe once she is back in the flock and he is the newcomer again that he will stop?

She may be a pet but you have 13 other pets and I'm sure you would be mighty crestfallen if the other 13 fell ill. If she were healthy she would stand up for her self a little, she knows she is weak and he knows she is weak, just because you gave her a broad spectrum antibiotic (with out running cultures) she doesn't show any major symptoms does not mean that she isn't still sick, she could still be a vector for disease to catch the rest of your flock. The only reason we have strong and healthy chicken breeds today is because the weak chickens were culled from past generations.

Brendan,

I totally agree and appreciate what you are saying and if I thought she were seriously ill or suffering I would do the right thing. She is in fact, perfectly healthy, happy and laying eggs like a hen should. I do think that if she had something contagious others would have shown signs by now as it's been going on for over a month. I am a responsible animal owner.

I agree with removing the rooster for a while. I have had the greatest success when one chicken in picking on another, by removing the aggressor.

They tend not to be so confident when you put them back in the flock, and it gives the one having a hard time a chance to regain confidence.