Changing position of an element that is being animated

Hey.
Does anyone here know how to approach this?

I have a walking animation, using Puppet2D with inverse kinematics. In it, the head has no keys, and apparently I'm able to interact with the head IK through code, which is great.
But, if I wanted to do this with an object that does have keys in the animation, they would fight, frame by frame, code vs animation.

Is there any way to override what's happening to this object in the animation, and let its position be altered by a script when I tell it to?

Here's what (well, one of the) I want to do:

-Let a walk cycle animate what's necessary to look good (like swinging hands).
-During a certain key press, let mouse Y position control the height of a hand IK.

I have many similar functions kind of dependent on an approach that will work in puppet land. Any suggestions?

 

Managed to solve the problem, using a method from here: http://answers.unity3d.com/questions/126368/how-to-rotate-a-bone-during-an-animation.html

Not sure if it's an entirely clean approach, but maybe still.
Summary: Perform any overriding user input over animations in LateUpdate() and try to keep the code in there to a minimum.