Do you do any form of pressure and release?
Medical reasons aside, horses throw their head because they find the release from the bit upwards. To get rid of this nasty habit you need to have the timing and finesse to retrain the horse to find the release when their head is down.
I would try a full-cheek sweet iron snaffle, so she can't get her mouth around the eggbutt. Or even ride in a rope halter and lead. Then I would say lateral flexion, lateral flexion, lateral flexion. And make sure you have good timing and big releases. That head needs to be so soft going side to side that you can have a pinky's amount of pressure for her to seek that release. If she throws her head up, keep the same amount of pressure until she comes down to an appropriate level. Check out some natural horsemanship videos for this.
Then you apply the same concept vertically. Hold, and keep holding if she puts her head in the air. The release is when she puts her head down. If you are afraid that she might flip, or begins to back up, push her through a medium sized circle. In the circle, use the rein low to push her through it. She won't be able to make a proper circle if her head is wild in the air. The moment she puts her head down and goes softly, loosen the reins and let her go straight.
The worst mistake you can make is when she throws her head up to instantly release the pressure.