There are two main reasons why it was very difficult (and maybe even impossible) to use military force to bring about social and cultural change in the Reconstruction era.
First, it was difficult to do this because it is never easy to force people to change their society or their culture. The South had, of course, had a system of slavery up until the end of the Civil War. That meant that social attitudes about race relations had been firmly embedded in people’s minds. There is no way to make people change their minds through military force. Unless you are going to do things like having a soldier present every time a black person interacts with a white person, there is no way you are going to change interpersonal behavior.
Second, it was difficult to change society and culture because the North was not firmly committed to doing so. The bulk of people in the North did not care a great deal about the situation of African Americans. Even whites in the North typically believed in white supremacy and did not really want equality for African Americans.
It was not really possible to bring about change via military force, then, because it is very hard to do so in any situation and it is even harder when there is no very strong support for the change in the first place.