I have asked an employer from six year ago to give me a reference. We had a good working relationship, and she has given me a glowing reference with regards to the work that I did. However... She is clearly miffed that I did not keep in touch since I worked for her, and the reference is overshadowed by her emotions regarding this.
Since my failure to keep in touch is a personal issue, and in no way relevant to the work that I did, or my ability to do this work, can she really do this?

She can say whatever she wants.
You can try to repair any damage done (you are very vague about what that might be) by explaining the story.
You don't have a lawsuit as far as I can see, unless you want to explain here.

You asked for the reference, there are no laws governing this. She can say anything she wants as long as she doesn't lie or defame.