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I would just get an exhaust suitable for an '05-06 coupe. It will either work with the cabrio right out of the box, or the most you might have to do is lower the cross-brace under the car by about 3/4". There's a picture of my lowered brace here.
Basically, it just involves using longer bolts, and a few nuts on each side as spacers. The nuts need to be bigger-diameter than the bolts, so that they'll just slide over the bolts rather than having to be screwed on.
I've done this mod on a couple of cabrios (both Cooper and 'S') with no problems. In fact, I've put about 50k miles and a few dozen autocross events on mine.