If both a Beasts and something that counts as a Beasts (e.g., a sacred site of Many Minds Move as One) are in the same land and something destroys a Beasts there, can you choose which one is destroyed?

If both a Beasts and something that counts as a Beasts (e.g., a sacred site of Many Minds Move as One) are in the same land and something destroys a Beasts there, can you choose which one is destroyed?

Yes. Even if there are two ordinary Beasts tokens in a land, players get to choose which one gets destroyed – it just doesn't usually matter which one you pick.
Similarly, if a Presence and an Incarna are both in a land and something would destroy Presence there, the Spirit can choose whether to destroy the Presence or the Incarna.