This is exactly why one would not use tracking markers. Have you tried keying them? Isolate the spot with a mask and try to key out only the orange. You could also try masking them out and then keying/masking only the hair back.
There are a few approaches but mine would be this:
Firstly, duplicate the layer.
On the top layer, isolate the orange markers with masks.
Set the masks to subtract.
Reposition this layer below until the masked area is green across the whole shot.
Precompose the two layers and use keylight to key out the green.
You will get holes in the resultant key where the markers cross the hair, so use roto brush or extract to repair.
You could also just paint the markers the same colour, but whatever technique you will have to roto the hair at some point probably.