1. When an animal is in your squad, it works the same as a human character in that you have direct control, you can select it and give orders.
2. Animals are AI controlled, they permanently follow and guard their master and you don't have much direct control over them.
So more like this:
When an animal is in your squad you can right click on its portrait, or on the main screen, and have either a box come up, or a list of commands you can give it. Or how about an entire pet window, with different options you can set so that it can be used for specific tasks, or set a group to do specific set of tasks. You should also still be able to click and have them move to an area, and while in that area, like say have an option to guard, and it will stay either in that spot or "patrol" around the spot so, to guard whatever you set it to guard. And what I like about this idea even further is you can load say a pack on it and send it to a character.
I would hate to limit the functionality of the animal, but cater to both types of players. That way both would get their style and everyone is happy