Congress gave the US military control over Southern state governments to

- To transition them into reconstruction and accept the establishment of slavery.

- To ensure that the formation of new southern government didn't became chaotic.

Explanation:

The control was given not long after the civil war was over, and the southern people were forced to let go of the slaves that they held and treat them as equal human being.

The central government realized that this won't be easy. There were still a lot of people who held a grudge from their lost in the civil war that could potentially do something harmful to the ex-slaves there.

This is why the Congress gave the US military control over Southern state. In order to prevent/minimize such occurrences.