This is really a very simple choice. How much do you love your girl? How much do you want to be around her?
If you're flirting is bothering her, and you care about her feelings, don't flirt. If you do anything else, you're sending the clear message that you don't care about her feelings.
Ask yourself what is each of your motivations? Likely, she thinks you are acting innappropriately and senses a threat to the relationship. That is why she wants you to stop. Because she values the relationship.
Now, why don't you want to stop? Because of personal inconvienience?
From the outside looking in, I think if you want to be with this girl and you have a commitment with her, then you should stop. If it's not a serious relationship, then continue to make decisions based on your personal comfort as opposed to the comfort of the relationship and the needs of both people in the relationship.
Basically, think about what you would have done when you first met her. For whatever reason, people tend to stop doing the things that brought them together in the first place.
Good luck.