Oh, so it's "war powers" now? You going to try to sweep suspensions of habeas corpus into a catchall "war power", and then claim that Lincoln has infinite authority if a gun goes off?
Oh, brother.
Where is Farber getting all the purple rhetoric you're quoting, anyway? (Let's pretend for five seconds he has any authority to put up against Scalia, who's saying Farber is full of it.)
The Prize Cases irrefutably recognizes the President's power to answer the insurrection and to meet force with force. It clearly states that the President does not have to wait for a Congressional authorization.
Congress, at least twice during the war, retrospectively authorized and ratified the President's emergency actions. Lincoln took decisive action, and the Congress and the Court backed him.
The text Farber quoted from Mitchell v Clark suggests that if Congress had was empowered to take an action before the fact, it could take action retrospectively. (Do not confuse this with an ex post facto prohibition - those deal only with criminal activity.) Mitchell also suggests that Congress had broad authority to make right any extralegal actions taken to deal with an emergency.
So even if you believe that Lincoln was not entitled to invoke the Suspension Clause, you must admit Congress was entitled. Congress was also entitled to "ratify what had been done" (Mitchell v Clark). Congress authorized the President to suspend the privilege of the writ of habeas corpus as his discretion and ratified his past suspensions (Habeas Corpus Act of 1863).
It seems to me, that if the Congress and the President are in agreement with respect to war policy, there is little at issue for the Court to object to.