I.. well.. I don't know, but I'm reluctant to hit the don't know button.
I think his heart is in the right place, for what it is he does.
But, what he does is questionable. Or is it?
Hmmm.. well, I seem to be talking bollocks. let me start again.
Nick Fury is under orders, so that should personally remove him from the question of morality. Given his voting habits have been mentioned (he voted Nader, not the last election), that means he is rebellious against the general running, and his personal politics are not part of the machine he works for. Which, makes him no so inclined to take orders, therefore throwing back some of the responsibility back to him. (sorry for the runaround)
On the hulk issue, I do firmly believe, justified or nay, that he perfectly intended banner to survive. (+1 fury)
On the Thor issue, he does his job. He has doubts about Thor, and sees a truth. One based on facts, one that I would, given my beliefs on such matters.(+0 fury)
The big downpoint for me though was allowing Cap into the Middle East, best of intentions maybe, but one as Fury, so armed with the facts, saving a few lives for a popularity hike is no great thing. He gets 1 point down on that one.
All in all, Fury though.. hmmm.. I think good guy. Though grey as hell. but such is war.