What argument can be made to say that the counterculture's emphasis on personal freedom damaged American society?
This is a controversial topic as much of our current “culture wars” can be traced to the changes associated with the counterculture and the ensuing backlash against those changes. Many people feel that the emphasis on personal freedom helped American society. They would say that it made our society less patriarchal and fairer for people like women and minorities.
That said, an argument can clearly be made for the point of view given in the question. Before the 1960s, we can argue, American society was much more stable. People were much more likely to believe that they needed to make personal sacrifices in order to keep families stable. Instead of giving up on marriages and getting divorces (one can argue) people put their own desires aside and stuck it out. This made society as a whole better because there were fewer children growing up in broken homes.
The main argument, then, is that our new emphasis on personal freedom has made us more selfish and less focused on what is good for society as a whole. Divorce is an example of that, but there are other examples in the economic world. People want to have all sorts of material goods right away and they overspend and overborrow to get them. This leads to things like the housing bubble that led to the financial crisis of 2008.
From this point of view, the ideas of the counterculture have produced a selfish society where people pursue their own desires even if, in doing so, they hurt us culturally and economically.