I don't think it's forcing children to separate, but it may be keeping children out of the class who are not really ready for the class. I homeschool and love spending all day with my kids, but I also value having other role-models in their lives. I get to pick those role models and if they're not working for my child, then I move on. I don't homeschool them and sign them up for classes so I can control every single situation and make it exactly what I want. If I don't like it, I find something I do like. If my 5yo doesn't want to be without me, then I'll find something for him that accommodates that. I would ask him to try it first and then if he doesn't feel comfortable, I would wait for awhile and try again. I want to show my children that I trust them to handle the situation.
Even in my 10yo's middle school class science class, I see parents doing things for their 10-14yo's. Really? Your child can't cut a piece of paper or use a hole punch??? The teacher is very active and knows how to engage the kids and he tells them step by step how to do the experiments and make the models. Still, the parents are there, doing the stuff for the kids. Drives me insane. I enjoy sitting in the class because the teacher is so funny. I sit quietly in the back because it's allowed. I would be fine (even happy) with them kicking us out of the class.
If it were a Waldorf class that didn't want an early academic class, I'd expect them to not sign up for an academic class...not to make the class less academic. Or not to take an organized tour if they really want to go at their own pace. I don't go on organized tours very often for that reason.
I think that if you let the museum know that you are not signing up for the class because you're uncomfortable with the policy, that will lead them to either change the policy or not. I often write emails and call the local YMCA to let them know what I like, dislike, would like to see in their classes. Often, I find that what I want is on the next session. We've had classes where we, as parents, have moved all of our kids to a different teacher or even facility when we didn't like what was going on...a teacher we found too rough, not disciplined enough, not engaging enough, etc. When 20 kids suddenly move out of a program, they take notice.
At 5, it's a different story of course. But if the museum wants the children to be mature enough to be without their parents, that's their call. I love homeschooling, but I want my kids to have their own, genuine experiences without me there as well.
I'm surprised at how many people here aren't bothered by helicopter parenting in the class setting.