答案--Android setFocusArea and Auto Focus
我所要做的就是取消之前所谓的自动对焦。基本上正确的动作顺序是这样的：

protected void focusOnTouch(MotionEvent event) {
    if (camera != null) {

        camera.cancelAutoFocus();
        Rect focusRect = calculateTapArea(event.getX(), event.getY(), 1f);
        Rect meteringRect = calculateTapArea(event.getX(), event.getY(), 1.5f);

        Parameters parameters = camera.getParameters();
        parameters.setFocusMode(Parameters.FOCUS_MODE_AUTO);
        parameters.setFocusAreas(Lists.newArrayList(new Camera.Area(focusRect, 1000)));

        if (meteringAreaSupported) {
            parameters.setMeteringAreas(Lists.newArrayList(new Camera.Area(meteringRect, 1000)));
        }

        camera.setParameters(parameters);
        camera.autoFocus(this);
    }}

.....更新

@Override
public void surfaceChanged(SurfaceHolder holder, int format, int width, int height) {
    ...
    Parameters p = camera.getParameters();
    if (p.getMaxNumMeteringAreas() > 0) {
       this.meteringAreaSupported = true;
    }
    ...
}

/**
 * Convert touch position x:y to {@link Camera.Area} position -1000:-1000 to 1000:1000.
 */
private Rect calculateTapArea(float x, float y, float coefficient) {
    int areaSize = Float.valueOf(focusAreaSize * coefficient).intValue();

    int left = clamp((int) x - areaSize / 2, 0, getSurfaceView().getWidth() - areaSize);
    int top = clamp((int) y - areaSize / 2, 0, getSurfaceView().getHeight() - areaSize);

    RectF rectF = new RectF(left, top, left + areaSize, top + areaSize);
    matrix.mapRect(rectF);

    return new Rect(Math.round(rectF.left), Math.round(rectF.top), Math.round(rectF.right), Math.round(rectF.bottom));
}

private int clamp(int x, int min, int max) {
    if (x > max) {
        return max;
    }
    if (x < min) {
        return min;
    }
    return x;
}