there doesn't seem to be much information out there currently regarding Moo2 and windows 7. I just came across this:http://forums.civfanatics.com/showthread.php?t=324477
this was obtained by doing google search 'masters of orion 2 running on windows 7'. The suggestion was to use DOSBox though I have never used dosbox.
Perhaps as time goes by more user data will become available as people with windows 7 try to get old classic games such as Moo2 working on the new operating system and a 'best solution' will be found. However there currently doesn't seem to be a best solution.
I remember playing Moo2 to death a few years back, at the highest level of difficulty it did present a challenge. A good starting position was essential, otherwise it was game over within the first few turns. However once I had finally mastered the game a couple of things did eventually put me off it. The first thing was it became quite easy to exploit the AI with the right technology, namely in ship-to-ship combat the ability to teleport troops from the player's ships to enemy AI ships and by that means take over the enemy AI ships and add them to the player's fleet. The second thing that put me off was the inability to use tractor beam technology in ship battles without the game crashing after a time. However the fault may have been due to modern and incompatible nvidia graphic card technology.
Might try space empires V next.