I'm sorry to hear about your horse. Its a really hard thing to go through. But you have done such a wonderful thing by taking her in as a rescue, I'm sure she is very appreciative.
In my experience, the injection is the best option. Its much easier for me to know that they went peacefully, instead of by using the gun. While in some cases, when its the only option, it can be done right, and supposedly the horse doesnt feel any pain.
This is a very hard decision to make. While I would choose the injection, i'm sure you'll do what's right. Good luck.
Melissa