I've taken both violin and piano lessons. Violin was far more physical - needed correct posture, hand position, etc to develop good habits, whereas piano didn't, not in the same way. So I wouldn't compare the two lessons. My violin teacher did have to touch me at times to adjust positioning - in fact, I wish it had been much more often, as I ended up with really bad habits, sore muscles, strains, etc, in the end. If I'd realised I was tensing my shoulders or twisting so much or whatever else I was doing, future problems could have been prevented.
So I'd not think it was unusual for a violin teacher to touch. I would expect him to tell/ask her if he could - I've heard teachers say "I'm just going to adjust your arms position, is that OK?" or "I'm going to check if your shoulders are relaxed, are you happy for me to do that?" etc.
I also remember thinking lots of 'older' (to me) men were slightly creepy when I was a preteen/teenager. I don't really know why. They wouldn't have been that old, either. But it was actually more that I was just slightly scared of adults, and men more so as I'd mostly had women teachers in school. It was just unfamiliarity I guess. But it would have made me uncomfortable, slightly, and I'd not have wanted them close or touching - but nothing to do with any of it being inappropriate. Just that I didn't like them all that much somehow. Even now, the idea of some physical contact (like hugs) from people either repels me, or is totally fine, and it's not that they've done anything wrong, or even that I don't like them, but I'm just not as comfortable with the idea of being close - it's like an instinctive reaction, a sensory sort of things. But based on nothing inappropriate.
So I can well imagine not liking certain music teachers to touch me, but that having nothing to do with them doing anything even slightly wrong or inappropriate. It was seriously just me and the way I was. I hate to think how me saying I was uncomfortable might have been misinterpreted!! Luckily I never did, just put up with it.
I'd say take her seriously and listen to her, by all means; find out what is making her uncomfortable, but don't assume that it is necessarily anything that the teacher is doing. Perhaps you can ask her first whether she would feel more comfortable if you were there - for me, that wouldn't actually have made the difference, as it was the touching itself that bothered me, not whether anyone else saw/knew or whether it would have led to anything further. I'd also have hated having my mum sit on my lessons long term, as it really changes the student-teacher dynamic, and I'd have found it much harder to learn with her there. No reason not to switch teachers if she does still find it uncomfortable - worth respecting her feelings about it - but I'd not make it out that he had done anything wrong (without proof), more just that there's a better overall fit with another teacher, if she finds one she prefers.