For all his bravado about how Section 31 is unjustified in what it does--the immense irony is, like Michael Corleone before him, he's constantly feeling led to do those very things he condemns, in order to take on those he sees as the enemy.
We also saw that in Sisko trying force Eddington's surrender. If he could led down that dark path, anyone could, even the person who would presume to lecture him the same way he presumed to lecture Admiral Ross. The common thread there is dealings with one particular enemy. Even Jack Bauer, who already makes up the rules as he goes, takes things a step further
in his dealings with Charles Logan.