I will preface this by saying it's not one I'm the most knowledgable about, but I may be able to give you an idea or two.

Lincoln was very critical of the Supreme Court after the Dred Scott v. Sanford case, in numerous speeches prior. It's possible that he was attempting to say that the Supreme Court would not and should not dictate the entire policy of the government, and that the federal government's branches should be able to do things outside the scope of the Constitution's strict limits in order to address things like slavery. However, he likely didn't want to say this outright while talking about slavery, because that would've only stoked tensions. However, I think you may benefit from the whole quote, which you may have but didn't include:

I do not forget the position assumed by some that constitutional questions are to be decided by the Supreme Court, nor do I deny that such decisions must be binding in any case upon the parties to a suit as to the object of that suit, while they are also entitled to very high respect and consideration in all parallel cases by all other departments of the Government. And while it is obviously possible that such decision may be erroneous in any given case, still the evil effect following it, being limited to that particular case, with the chance that it may be overruled and never become a precedent for other cases, can better be borne than could the evils of a different practice. At the same time, the candid citizen must confess that if the policy of the Government upon vital questions affecting the whole people is to be irrevocably fixed by decisions of the Supreme Court, the instant they are made in ordinary litigation between parties in personal actions the people will have ceased to be their own rulers, having to that extent practically resigned their Government into the hands of that eminent tribunal. Nor is there in this view any assault upon the court or the judges. It is a duty from which they may not shrink to decide cases properly brought before them, and it is no fault of theirs if others seek to turn their decisions to political purposes.

Source: http://avalon.law.yale.edu/19th_century/lincoln1.asp

So, examining the whole quote, I think the message becomes clearer, and that he's likely referring to the question of constitutionality of slavery being a big issue, but not one that the people should only rely on the Constitution for, or the Supreme Court. This is clearer when we look at earlier in his speech (so little earlier that it's almost certainly tied into the subject):

All profess to be content in the Union if all constitutional rights can be maintained. Is it true, then, that any right plainly written in the Constitution has been denied? I think not. Happily, the human mind is so constituted that no party can reach to the audacity of doing this. Think, if you can, of a single instance in which a plainly written provision of the Constitution has ever been denied. If by the mere force of numbers a majority should deprive a minority of any clearly written constitutional right, it might in a moral point of view justify revolution; certainly would if such right were a vital one. But such is not our case. All the vital rights of minorities and of individuals are so plainly assured to them by affirmations and negations, guaranties and prohibitions, in the Constitution that controversies never arise concerning them. But no organic law can ever be framed with a provision specifically applicable to every question which may occur in practical administration. No foresight can anticipate nor any document of reasonable length contain express provisions for all possible questions. Shall fugitives from labor be surrendered by national or by State authority? The Constitution does not expressly say. May Congress prohibit slavery in the Territories? The Constitution does not expressly say. Must Congress protect slavery in the Territories? The Constitution does not expressly say.

It seems to me Lincoln is, in a roundabout way, trying to dismiss secessionists' claims that the Union has denied them rights, giving them the right to secede.

So basically to sum up this rambling comment, my interpretation of it is that Lincoln is trying to say that the Constitution doesn't cover everything, that the secessionists' are wrong in saying that the Constitutional rights they have are abridged, and is criticizing the Supreme Court by minimizing its power in his speech, saying that government policy can't only be based off cases like Dred Scott while also saying that people are looking at Dred Scott as setting a precedent when it does no such thing (hence the "it is no fault of theirs if others seek to turn their decisions to political purposes." that follows).

Does that make sense? Or should I try to reword it :P.