if karzai was a legit problem he wouldn't be in charge much longer. he also has very little control over his own country. he is the mayor of kabul, but certainly doesnt have a monopoly on violence with in his country. if push comes to shove he also doesnt have much of a military do anything with either at present. country is kind of in tatters. civil "strife" for half a century or more does that. imho its not really worth worrying about. hes just posturing.
EDIT: keep in mind the US is pulling out of the region while pakistan will be there for a while, and there is already concern over Pakistan shelling allied and afghan troops
EDIT2: also look at it from the afghans point of view. we came bringing war and conflict, not that life under the taliban was roses, and a lot of innocent afghans civilians have died. we are also meddling in their government again, which most peoples in general dislike. we also havent removed karzai even though its pretty apparent that the last election was rigged by/for him.