I actually think this manga provides one of the more interesting and subtle analyses of patriarchy in media I've seen in quite some time. Here's my interpretation.
I think basically the hunters and the beasts represent the two sides of patriarchy. The ideal of patriarchy is a strong man protecting weak women from evil men, right? So Kemono Waltz kind of represents that world literally: there actually are beasts out there who will murder young girls unless a hunter protects them. But as we also see, what patriarchy promises women is not freedom but subjugation: inequality as a superior alternative to destruction. Both Meiko and Minami are rebelling against this status quo, Meiko due to her abusive father and Minami due to her family trying to control her life, which is why both are "beast allies." But their common weakness is that they cannot imagine a life outside of being consumed; as such, the best they think they can hope for is to choose who consumes them, a prospect they even eroticize.
What Shirayuki offers, in that sense, is an alternative. As someone with power who is simultaneously herself a victim of the patriarchy (as we can see even from the short snippets we get of her talking with her brother), she's in a unique position of being someone with the power to affect change who lacks an interest in upholding the mutually reinforcing hunter/beast patriarchal status quo. The problem is that, at the beginning of the manga, she seemed without any real goal or desire; she acted the part of the school prince, flirting with girls and defeating beasts, but didn't seem to get any real happiness or meaning out of it. Meiko, I think, appeals to her because she's also someone who exists outside of the "brave male hunter/innocent female damsel" model her society offers her. So the question is whether together they can find some way out of this mess that doesn't involve self-destruction.