I have a theory that the Blackstaff can removed ALL black magic taint from it's user. Even taint that was gained prior to the Blackstaff's acquisition.
Therefore, it's possible that Eb did some horrendeous things before acquiring the BS, and the BS cleaned him up aftwards.
I'm not sure I buy that Eb was walking around with the taint of having caused hundreds of deaths on him for eighty-odd years between New Madrid and gaining the Blackstaff, apparently as captain of the Wardens for a chunk of that time, and nobody would have noticed something wrong with him.
Although given the WOJ that the Blackstaff chooses his or her own successor, it's possible they'd be heavily biased in favour of one of their own apprentices as the person best trusted to use it responsibly. I wonder if the collection of journals is not just a chain of masters and apprentices, but Blackstaffs and their chosen successors? In that case, New Madrid might have been an act of Ebenezar's predecessor, or the predecessor loaned a trusted apprentice the artifact for one-time use for some compelling reason.