In any case, transformation is often a symbol of change and growth. Most often, for the magical girl, transformation is a form of empowerment. Through it, she receives abilities that a mere girl lacks. Frequently, especially in idol magical girl series (though it's observable elsewhere, even to some extent in Sailor Moon, if one will recall the Luna Pen), the girl will literally transform into a woman. She may or may not actually have any powers at all other than transforming into a different shape, but in this form, she can enjoy the freedoms and opportunities that being an adult presents. The girl gets to remain a girl, but issues are bound to arise from this double life. As far as magical warrior series, the girls don't usually (but can) physically age, but Sailor Moon is a good example. We know Usagi's future: she will become the graceful, elegant leader that is Neo Queen Serenity. That figure is a far cry from the childish crybaby Usagi. However, we get glimpses of the strong woman Usagi is destined to grow into throughout the series, particularly when she is fighting as Sailor Moon. Usagi and the other girls accept their responsibilities and their destinies and grow because of it.
I would argue that coming of age is normally treated as a positive thing in magical girl shows. Although it brings many hardships and can be rather bittersweet, it's still looked on as a necessary process, and the girls that undergo it are heroic figures.
This is not how it works in Madoka, obviously. The thing that really connected the dots for me was Kyubey's comment at the end of 8: "In this country, growing young women are called girls [shoujo]. So it's only proper that you, turning into witches [majo], should be called magical girls [mahou shoujo]." The signifance is thus: the characters in shoujo are "little/small" and "woman," and it specifically refers to a young girl, no older than 18. Majo, on the other hand, is made of the characters for "magical" and "woman." Keep in mind that they could have called witches "majokko" which also means witch but carries the diminutive -ko, making it interchangeable with mahou shoujo. They did not. As magical girls become witches, so do girls become women.
There are various implications this could have, but I think the theme here is being forced or lured into growing up too fast and the destruction of innocence and happiness that comes along with it. By what, exactly? Well, various things. For one, trauma. On the literal level, we see the effects that trauma has on the girls. For another, society. Look at their school: it's modeled after a prison. An actual prison. Furthermore, we have the men in 8 who casually badmouth women. Japan is still a pretty patriarchal society, and that's just one more huge source of pressure for girls and women. There are a lot of other possibilities too, but those are the ones most easily apparent to me, looking at the series.
Some other things to note are certain rune translations:
"The blooming roses shall be presented to the queen immediately."
"The first buds shall be plucked."
So, what do you guys think? I'm definitely going to keep this interpretation in mind as I continue to watch.