Let her settle in first before you wean her. A LOT of people don't touch their babies until they are weaned, so you really don't have a problem. It isn't even a case of her past that is causing this. She is just an unhandled baby. No big deal. Separating now isn't going to help her become less afraid. Her momma is her safe place. She isn't being bad at all. She just doesn't know. It is also extremely common to wean at 6months, so unless she is pulling down the mare's health to the point where what you are doing isn't helping, I'd leave her where she is safe.
I would ignore her for about a week and work with momma. Get to know her, get to know how defensive she is, how protective of her baby she is, how inclined she is to kick, and all that, and really, just ignore the baby. Don't try to touch her or look at her(other than the once over daily wellness check), or anything. Just go in, and do what you want to the mare. Just go in and groom the mare, fuss over her, do what you do as if the baby wasn't there. Now don't go in shaking a tarp and jumping up and down with a bag whip to desensitize her right now, just do simple things. Do this for about a week, of total interaction.
Getting to know momma is great because she can easily become a fence in the stall. If you absolutely have to have a halter on the baby now, you can use the mare to trap the baby long enough to get a halter and lead rope on her. It is best if know the mare isn't going to eat you for messing with her baby.
Other than that, right now I would suggest doing a search on here for "halter training foal" and see what you can find.
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