When I first got Jack (he was 7 mo. old and had lived his entire life outdoors) he had terrible ear mites. Back then the only thing they could do for him was use eardrops twice a day. The mites were so bad that we had to do this twice a day, EVERY DAY for 40 DAYS!! Needless to say he really hated having his head touched or his ears scratched or even to be held. We would have to wrap him up in a bath towel to get the drops in because he'd learned to hate it. It took him a long time (a year or longer) to warm up to having his head touched or be held, however now he's as affectionate as they come (he's 6 now), and LOVES to have his cheeks and ears scratched and be petted on his head and will give you a 'head butt' when he wants attention. He's even become a lap baby!!

There's always hope for your kitty, just be patient and go slowly and I'm sure she will come around.