What type of bit are you using.
I know we all wish every horse would be a peach in a snaffle, but occasionally you have to step it up a little to teach that whoa means whoa. I've found that with some that had a dicey background like yours may have had, that I have to teach "backwards," in a way.
After I develop a decent stop with a pelham (with two sets of reins), or some other bit with curb action, I can often reduce the potential severity of the bit and go to something with less or no leverage.
You need to be safe, of course, or you will be of no good to this mare. And, the mare will find working less stressful when she learns to respond better to what you need her to do.