Ideally what you want to see with emissions standards, is simply an alteration in buying habits caused by an alteration in what is being marketed to and made available to people. You would hope that the costs associated with the standards would be made up for by the reduction in unnecessary fuel consumption, and by auto manufacturers making more appealing cars due to their R&D efforts, and thus having increased sales. That last part is questionable, but in the long term, I imagine the R&D efforts will end up saving auto manufacturers money simply because they will save money in terms of fuel costs (which seems somewhat ironic).
Now, I will agree that now seems a bad time to be implementing emissions standards, but companies have until 2016 to comply with the California law (I believe); and I do think such standards will improve the economy in the long term. Plus, automakers know they're coming eventually, so they're going to spend money preparing to comply regardless of this particular action on the part of Obama.