I know it's hard for we jock types, but we have to listen to our bodies: your daughter isn't ready for the type of exercise she's doing.
The doctor who attributed her symptoms to poor conditioning is, frankly, an idiot. Exercise induced headache is a fairly common PCS problem. I have to work out with a heart monitor. If I let my heart rate exceed my PCS comfort zone, my blood pressure spikes and my head feels like it's going to explode. I worked out with my PT to determine my safe zone. Frankly, it's not much compared to my premorbid frenized fitness routine. Still, it's better than nothing.
I'd suggest your daughter work with a professional to determine the type, intensity and duration of exercise she can handle. Zero impact activity done for a couple minutes a few times a day is usually a good start.
Patience