Just go to the Zivilamt and process the civil wedding. I think there's a 2 week waiting period, but once that's done all but the most overzealous rubber stampers will leave her alone.

I don't know the exact legality on it, but it's referred to as the right to family reunification, so being in a legitimate, legally endorsed relationship with a Swiss citizen would pretty much tie their hands. Yes, they may put you though a few spot checks to make things difficult - but if it's actually legitimate, there's nothing to really worry about.

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The red blobs are all mine, you can't have 'em back!!! Bwahahaha!!!