I don't know if it will play well with locomotion or not, but I've tried it, and scripting the character controller collider DOES work... At least changing the height and center of the collider.

I created a small example project, but can't upload it here, so if you need it send me your email using a private message or something.

The code attached to my character controller:

using UnityEngine;
using System.Collections;

public class Crouch : MonoBehaviour 
{
    public  Transform           tHead;

    private Vector3             _v3InitialPosition;
    private Vector3             _v3CrouchingPosition;
    private CharacterController _characterController;
    private float               _fInitialControllerHeight;
    private float               _fCrouchingControllerHeight;
    private Vector3             _v3InitialControllerCenter;
    private Vector3             _v3CrouchingControllerCenter;

    void Start()
    {
        _v3InitialPosition = tHead.localPosition;
        _v3CrouchingPosition = _v3InitialPosition + Vector3.down;
        _characterController = GetComponent(typeof(CharacterController)) as CharacterController;
        _fInitialControllerHeight = _characterController.height;
        _fCrouchingControllerHeight = _fInitialControllerHeight - 1f;
        _v3InitialControllerCenter = _characterController.center;
        _v3CrouchingControllerCenter = _v3InitialControllerCenter + Vector3.down * 0.5f;
    }

    void Update () 
    {
        if (Input.GetKeyDown(KeyCode.Space))
        {
            tHead.localPosition = _v3CrouchingPosition;
            _characterController.height = _fCrouchingControllerHeight;
            _characterController.center = _v3CrouchingControllerCenter;
        }

        if (Input.GetKeyUp(KeyCode.Space))
        {
            tHead.localPosition = _v3InitialPosition;
            _characterController.height = _fInitialControllerHeight;
            _characterController.center = _v3InitialControllerCenter;
        }
    }
}