You can disarm and utterly control them only if you repress them and make them work at gunpoint, otherwise they would be capable of rebellion, sabotage, assassinations & such.
A well educated alien population wouldn't be as eager to do intellectual/skilled work for an invader, and you wouldn't certainly trust them with strategic job positions (you wouldn't want them anywhere near your ships or weaponry, and you wouldn't let them manage your research or your wealth), so even if they are educated, you are forced to view them as slave labor for mines, factories and other dangerous places. They are "productive" only in that sense.