I daresay nobody had control over the timing. The cases were first litigated back when Newsom started issuing marriage licenses in the city in 2004, and the Supreme Court granted cert (or "review," as it's called in California) in 2006. It was just bad luck for them that it happened to get on the docket during an election year.

I think the secession advocates were just crazy fringe types. The SF Chronicle likes publishing them for unfathomable reasons. What they really did after the 2004 elections was to start donating money to the Democrats in reams.