Nick Fury seems like a tough customer from my limited knowledge of him, and from his bio. This is certainly a tough test for the Doctor. But even though Fury has (what, say 90 years?) fighting experience, the Doctor has ten times that.
The last remaining Time lord is over 900 years old, fought against every type of enemy imaginable. Robots, Mutants, Cyborgs, Priests, Vampires, Blobs, Living Plastic, Werewolves, Fish-People, Lizard-People and many many more have fallen to the superior intellect and strategy of the Doctor.
People have argued that the Doctor doesn't kill... well, they're wrong. He has killed in almost every episode of the new season, and when he didn't it was because his female companion begged him not too.. I'm not saying the Doctor would just whip out a Preacher MKII energy gun and have a mexican standoff with Fury because he'd likely at least be forced to regenerate (unless of course he uses his severed hand to channel the regeneration energy and stop the process, keeping the same form and avoiding incapacitation.)
But what if the Doctor uses his infinite knowledge of creation, his ability to see everything there ever was or ever will be, to stagger his steps, avoid a few (likely very well-aimed) bullets from Fury, use the vortex manipulator he happens to have lying around to jump one second back in time, choosing to land right behind Fury? Fury would watch the Doctor disappear just in time to get an energy beam in the back of the head, or The Doc could drop a small amount of unstable material, vortex manipulator away, detonate with the Sonic Lance?
Nick Fury is no joke but I think the Doctor, the man who trapped two entire species in a "time bubble" (For lack of a better term) to win the war for the whole of creation, can get the job done if anyone can.
Vote for the man who's people created black holes. Vote for the man who always overcomes the odds. This isn't a 60 minute episode of Dr. Who where he bumbles about fretting over some female. This is a war, and The Doctor fucking wins wars.