What you are doing isnt far out of the pipeline techniques that we have implemented at the studio Im at. In a nutshell, you create an asset as a separate file and each one is then referenced into the scene for animation. This way you can make a change to your original file and its updated in the scene automatically.

So if you want to get your dudes into a scene and animate them and as you've stated you need one smaller, simply create a group node and put the character in the group, you can then scale the group node, but just dont freeze the transforms after, it will screw the rig. Its a quick cheat if you dont wanna re-rig it. You should then see the character scaled in the referenced scene.

Jay