After Wednesday's ruling, it should be clear that we're past the point of "when the president does it, it's not illegal." The law of the land now is that when anyone in our professional intelligence services crosses the line in the name of national security, it's not illegal, or it's illegal in name only. To be able break the law with no credible threat of sanction is about the same as having no law at all.
It's hard to conceive of a more direct and devastating failure of the separation of powers than Congress, the president, and the courts all agreeing that the government can kidnap people and send them off to be tortured on mere suspicion of terrorism, that the innocent harmed through this process have no access to any kind of legal remedy, and that the perpetrators themselves have proved thus far to be immune from prosecution, as long as the government asserts that the matter is a "state secret."
Andrew Sullivan writes that changing this "will require a citizenry so enraged and protective of its core liberties against this security Leviathan that it compels dismantling this machinery and exposing it to the light of day -- not recklessly, not abruptly, but by close examination, judicial review, press inquiry, protest." I wouldn't hold my breath for that. While the Obama administration's embrace of the Imperial Presidency in terms of actual policy has been near total, there are important legal technicalities that leave the whole construction vulnerable. Namely, that the Obama administration has said that these powers stem from Congress, they're not inherent to the executive branch. They come from Congress passing legislation like the Authorization to Use Military Force.
That seems like a pointless distinction at the moment. But I don't think it will be ultimately. Impunity for lawlessness in matters of national security won't end through popular means, because scaring people is easy and policies that project "toughness" against a mysterious and frightening ethnic other are politically effective. But eventually the executive branch will do something to infringe on the priorities or prerogatives of one of the other co-equal branches in a manner that provokes a confrontation.
Basically what has to happen is the executive has to make Congress angry enough to rein in the executive branch, because at this point Congress can shut down the party whenever it wants. Between skittish Democrats and Republicans who think the only possible abuses of power come from the expansion of the welfare state, it's not likely to happen soon. But it's the only way I see things changing.