I think you'd have to put your clipping on something that isn't scaled, something like this perhaps...
<defs>
<clipPath id="myClip">
<rect x="0" y="0" width="200" height="200"/>
</clipPath>
<g id="myGroup">
<circle id="bb" cx="100" cy="100" r="120" stroke="#ff0000" fill="#0000ff"/>
<circle id="cc" cx="150" cy="150" r="90" stroke="#00ff00" fill="#ff00ff"/>
</g>
</defs>
<g clip-path="url(#myClip)">
<use transform="scale(2)" xlink:href="#myGroup"/>
</g>