If the Mysterons are supposedly peace loving aliens as mentioned in the first episode, why would they try to take over the Moon? They must have killed the Lunar Controller and Orson before the arrival of the Spectrum agents.
The Mysterons imply that they share a curiosity about the universe and possibly saw interest in moon colonisation, but supposedly abandoned this when Earth got there first.
But now that the War of Nerves is underway, they likely took control of the Moon colonists with the intent of building the Crater 101 complex to move their planetary forces closer to the Earth. One or two agents, or the hijack of a machine is one thing, but having a base of operations closer to Earth than Mars would give them possibly the power to make the events of "Attack on Cloudbase" a reality.