The argument against civil unions is a non-starter. You can resolve it the same way the first Congress did when it came to establishing a system of common law. What they said was simple: to the extent that existing English Common Law was compatible with the Constitution it would be rigorously upheld, with a rule of lenity applied while the incompatibility bugs were worked out, to the extent possible under the Constitution.

Same applies to civil unions. A civil union will be entitled to all the legal protections and privileges afforded previously to marriages, to the extent those protections and privileges are compatible with the new civil union law. In the event of clear contradictions, the old marriage laws would apply to civil unions until such time as the legislature explicitly clarified the issue, to the extent possible under the state constitution.