No, it sounds perfectly fine, although it certainly reveals your opinion that reunification was a difficult, even painful process, with significant consequences. It also assumes that you believe "reunification" is complete.
It does not, however, indicate you feel reunification in itself was a bad thing. For example I can say:
The Marshall Plan was an American initiative to help rebuild Western European economies in the aftermath of World War II.
Here, "aftermath" suggests that the war was certainly terrible, but it does not suggest it was wrong.
While "aftermath" is always used with significant and unpleasant events, it can be (somewhat) ironic:
In the aftermath of the tumultuous wedding, the young couple escaped on their honeymoon with only minor injuries, leaving their families to pick up the pieces.