Yep. EA sits firmly on the rights to SMAC, and as long as that's the case, there won't be a sequel.
What we
could see someday is a sequel in spirit - similar setting, similar gameplay, but different name and characters. Hard to do, but possible - though unlikely. SMAC simply didn't sell well enough (despite the huge success in reviews) to make the idea appealing to any publisher who wants triple-A games.
The only halfway decent chance I see is that an independent publisher with a decent established fanbase makes a SMAC clone. Stardock might be a candidate, depending on how well "Elemental" fares. Perhaps we should bug Brad Wardell with the suggestion.