"That would be just what the US would want"
I suspect that the Commission, in whole or in part, also wants this, because the commissioners are directly appointed by EU member states and as such are more likely to be out of touch with EU citizens and their privacy demands, and more favourable to business interests that want free data movement.
In any case, bottom line is, as long as the US Patriot Act is in place, any and all agreements that allow companies to store EU citizens' data on US soil will fall foul of the ECJs ruling. The problem isn't Safe Harbour, it's the 'secret court warrants' provision in the Patriot Act. Which, by the way, are very harmful to the US in countless ways.