Though 501(c)(4) organizations are barred from a certain scope of political activity, it is quite possible that many of these groups would qualify due to the very restricted definition of political activity imposed by the courts—though it strains credibility to think that any Karl Rove (or Jim Messina, for that matter) organization would be properly thought of as nonpolitical. Nonetheless, it is a critical responsibility of the IRS to make sure that politically motivated groups seeking to avoid the congressionally created disclosure requirements (really the last piece of federal campaign-finance rules to survive Citizens United) meet all the tests of 501(c)(4) status. The fact that IRS staffers were willing to do more than look behind simple paper applications and test the veracity of claims is nothing more than government doing its job.
So good for the IRS for rousing itself from its long slumber.
Yes, they screwed up badly, maybe because their investigative skill set is so rusty from disuse. Their failure was not that they scrutinized too hard or too many, but that they scrutinized too few. If the IRS had more evenhandedly and more widely reviewed applications for 501(c)(4) status, this would have been a singularly worthwhile effort. Instead it has been a disaster for the IRS and the Obama administration. And there are implications here that extend beyond this specific case and beyond partisan politics.