I doubt they could outrun a thrown kunai......even if they could Minato isn't travelling the speed of the kunai. Hes simply going wherever the kunai is at the moment he uses his technique. Its instantaneous travel. Nothing is faster than that.
Madara going anywhere in the world is distance not speed. If you were to compare Madara and Minato going to the same spot I believe Minato would be able to travel there faster. (granted the spot is within kunai distance).
What I meant is, for example, if Minato is standing somewhere with kunai in hand fighting an enemy. He is only as fast as a thrown kunai in a way. Because once his enemy sees the kunai coming he can get out of the way. Minato might throw 10 or 20 kunai out to cover the ground, the enemy can just back away onto fresh ground. Unless Minato regathers kunai or has infinite kunai, eventually he'll run out and the two fighters will be on equal footing.
So for a skilled opponent I don't think Minato's kunai trick would be to difficult to conteract, supposing that they knew about it and had a few moments to strategize. Minato's main advantage with this is lessened significantly if the enemy understands the kunai's connection to his teleport ability. Just my 2cp.
Peace