The mention of the ex post facto clause is long gone from the Wikipedia article (which is undergoing a lot of revisions today for some reason or other). A version which may or may not be the one you originally linked to is here, though since the quote is sourced to The Advocate, I don't know how representative it is of constitutional jurisprudence in California's circuit. Generally, the ex post facto clause is applied to criminal rather than civil issues, which makes me a little skeptical, but it's not an issue I've researched.

To put it to a court test would also likely require finding a substantive legal issue in CA where marriage would allow something that civil union wouldn't. Since I believe that civil union in CA gives couples all rights under state law that marriage does (and CA same-sex marriage never gave same-sex couples any marriage rights under federal law), that may be difficult.