I don't think you can take them over as such.
You gain resources from them via two ways. You either gain wealth by "taxing" their produce because they repreesnt private civilain initatives. Or you directly purchase their mineral output and it will begin to stockpile at the location of the colony. Civilian colonies come free with their own mass driver so you are also able to send their resources to your main colonies in the same star system straight away.
The civilian operation will only disband once all the minerals at the location have been extracted. If you "abandon" the colony you will erase their presence as well.
Hope that clarifys things