The first half of your post sounded to me like your therapist may have been trying to show you that you have her support, in which case paying her back without her asking may be a rejection of that support.

However, by the end of your post I grew concerned. While I agree that this isn't a good way of handling conflict and while I think a therapist's comment can help you see how other people ight also perceive your actions, I worry about your freedom to be yourself in therapy after being given so much for free. This is exactly the reason why therapists aren't supposed to bend over backwards and accommodate clients for free on the long term or give significant gifts etc. Her generosity is lovely, but only as long as you are still welcome to therapy with all of your frustration, anger, and whatever else you may be feeling. Therapy is supposed to be a safe place where you can look at your impulses and emotions and explore them, not a relationship in which you "owe" the therapist for favors.

Now, you're the one who's there and only you can know what's best for you and what's feasable in your situation. Would you feel freer if you gave the money back? Would you want to continue with this therapist, whether or not you give the money back? I think an open discussion about options would be best here, if you are willing and able to trust your therapist with this.