She just has to get used to it. I would twitch her, it just makes life easier and she should eventually calm down enough that you don't have to.
My horse gets shots once a month so he is really used to it. I almost don't even need to halter him anymore.
My mum's horse hates needles and he gets very scared, to the point where for a time he would get dangerous. We twitched him just because he is so big. Now he is much better and only needs a halter and a corner to be backed into to get his shots.
As long as you aren't abusing the twitch and using it for everything, it should be fine. Chuck it on, give the shots, take it off, give her cookies. Eventually when she stands super quietly just take it off.