Have you seen how cute our animals are? Look into the cow’s lashy eyes and tell us you would lock it in a Warehouse instead of allowing it on your farm.
As far as trees go, we wouldn’t deprive them of natural *cough* sunlight. However, we are looking into solutions for this, but they will require some future game features.
Meanwhile, finding a new home for them by selling (and losing a few coins, as a consequence) is a natural part of the gameplay. Conceptually, you can view this as everything in life has a cost (be it time or money), and rearranging your farm to make something else has this added cost.
HOWEVER we are working on a solution that will solve all the problems with space on your farm and will include the trees and animals too. 🙂