My advice is to STOP using the clicker. Your kitty isn't going to respond to a sound she doesn't like.
TONGUE AS CLICKER: I have "clicker trained" my cats using my tongue as a clicker. I put the end of tongue to the roof of my mouth and make two quick, successive clicks. You have to be sure to make the exact sound each time. Using this method, you can soften the sound so it is more pleasant to your cat.
SHORT SESSIONS: Remember, clicker training a cat takes some patience and time. You need to keep your sessions very short and repeat each day. (There is nothing a cat likes more than everything happening the exact same way everyday.) Basically, if the cat is finished with the session, you're finished. You try again the next day. Trying to force a cat to participate or getting frustrated at your cat will not work.
NATURAL MOVEMENTS: Also, I'm not sure what you're trying to train her to do, but remember you have to use the cat's natural movements.
Clicker training can be a great bonding experience between you and your kitty. Best wishes to you both!