Karmic Destiny is the "tendency of all things, when left alone, to trend towards becoming worse" that Urobuchi was referring to in his semi-famous quote.
It's the idea that things have consequences, and that there's no such thing as a free lunch. Kyubey was trying to game entropy, but the system he created still operated on fundamentally similar principles, even if it was anentropic - there was a balance of sorts between hope and grief.
Madoka's wish upended this larger system, which is intentionally set up to be a juxtaposition to how Kyubey violated the system of entropy - only instead of doing so selfishly, for her own ends, Madoka took the opposite approach, and personally took on the burden of all the grief in the world, thus setting her up as the antithesis of Kyubey.
It's actual, legitimate poetic irony.