Lincoln was surely aware that in suspending the writ, and ignoring Taney, he was exposing an underlying tension built into the Constitution itself, between the rule of law and the necessary power to preserve that rule in a time of crisis. The power of preservation has to exist somewhere, and Lincoln obviously thought it rested—at least initially and principally—with the person of the chief executive.
If there were to be any check on such sweeping presidential discretion, Lincoln said it would ultimately come from public opinion. “If [the president] uses the power justly, the same people will probably justify him; if he abuses it, he is in their hands, to be dealt with by all the modes they have reserved to themselves in the constitution,” said Lincoln in a letter responding to queries about the suspension.
Note that Lincoln’s response is distinct from, or more accurately, a modification of John Locke’s discussion of executive prerogative, in which an executive facing an extraordinary situation will act without the cover of law or even against standing law in order to preserve the state. According to Locke, this assertion of power resides outside the existing constitutional framework and, as such, is ultimately judged by the public accepting or not what the executive has done. The danger is that an executive, having had his actions approved, or more likely benignly accepted, will more readily act outside the law with justifications for doing so that are less and less tied to true necessities.
Lincoln does not ignore the role of public opinion, but he directs it back into and through the constitutional order. Not only does Lincoln take care to ground his suspension of the writ on a reading of the text of the Constitution, but he also suggests in his letter that there are constitutional modalities for judging and even modifying what he has done.
Elections, congressional control of the purse, and impeachments are the most obvious mechanisms Lincoln had in mind. Indeed, one reason Lincoln was so insistent that there be elections in 1864—despite the war still going on and his own decline in popularity—was that it reinforced the idea that the Constitution was still up, running, and controlling. He was willing to wield great power but careful to have it seen as much as possible as not being arbitrary.