I haven't read THAT closely but will chime in anyway.
I often hear friends whose kids are between about 2 and 3 1/2 talking about how their DCs are learning aggressive behavior from peers. My son, who is now 5 1/2, was a little precocious with aggressive behavior (lol... but he also got over it younger than many kids) and was for a while frequently pointed out as the kid who was "teaching" others to hit, push, etc. I had to accept that he apparently learned it all on his own. He was also an early talker, and definitely resorted to aggression with peers when frustrated by their lack of communication-- among many other triggers.
My thoughts are basically that the aggressive behavior is pretty normal for this age range. Sure, maybe being in a social setting brings it on earlier, but maybe not. You can't really know. Social settings also give LOTS of opportunities for learning to manage conflict and if the adults there are active in teaching conflict resolution skills and use non-punitive methods to manage toddler conflict, then the good may outweigh the negatives of witnessing or engaging in more aggressive behavior. I noticed that by 3 or 4 many of these supposedly "aggressive" kids seem really good at playing with same age or different age peers.
My son has always been in mixed-age classrooms (very part-time, play-based nursery for 1 1/2 years, then Waldorf Kindy, he's in his second year), and there is a nice mixed-age group of kids in the nieghborhood who frequently play in unstructured, lightly-supervised ways. DS very much looks up to and admires the older kids, and when he was younger, he definitely followed them about and engaged with them (or not, if they ignored him!). By 3 1/2 or 4, I noticed he began to choose same-age boys to play with, if available, but otherwise is perfectly happy to play with older or younger kids.
One final thought is that kids aren't always the most reliable reporters on what they are doing. My son NEVER talks about playing with the girls in his class, never mentions doing crafts, cooking, etc. Rarely mentions story time or singing. He pretty much ONLY tells me a blow-by-blow account of the war, fighting, and chase games he played with a particular group of boys (mostly older). But when we had our parent-teacher conference, the teacher was telling us how well he gets along with everyone, plays with girls, boys, younger and older, large groups, small groups. She talked about how engaged he gets in the crafts, how attentive he is during circle and how he sings with gusto and accuracy every day, etc. I mean, she *could* be making it up, but I think that my son just tends to relate the things that seemed most "exciting" or are somehow top in his mind at the end of the day. I mean, if I explicitly ask about the songs, or the girl he sits with at snack, etc, he has stuff to say.
We chose a waldorf kindy for our son-- actually, he chose it-- he is certainly not profoundly gifted, but did test out right on the line for being "highly gifted". He is very physical, and has always been extremely coordinated (gross and small motor) for his age, so perhaps that is part of why Waldorf has been a good fit. But I haven't noticed him being kept down or anything by the adults. My personal concern w/ Waldorf for gifted kids would be with grades. The early childhood classrooms that I have seen tolerate a whole lot of child-directed activity and a lot of variation in skills and behavior from the kids. I also visited 2 Montessori schools, one of which I liked a lot, where the kids seemed really engaged and to have a ton of choice in what they were doing, the other which seemed rigid and focused on pushing the kids to be "advanced". My feeling is that a rigid teacher, or otherwise inflexible classroom, regardless of the pedagogical approach, might not be a whole lot of fun for an inquisitive, experimental youngster.
If you sense your daughter is unhappy, or that the teachers are viewing her negatively, you shouldn't keep her in the school. At her age the whole point is to enjoy it, if you don't really need the childcare. You may be able to set up a rotating playdate or something, with 1 or 2 other families, so you each can take 1 morning a week off.