I love it! Never really occurred to me to do this with my Army Men figures. What a hoot!
I convinced a member of our gaming group to put together a similar game, several years ago, with 6mm toys. The group is die-hard historical, with occasional forays into fantasy battles. Only the organizer, and myself, knew there were aliens on the table! The battle was a what-if battle between German, and American forces, within a town. I controlled the Alien forces, and I started the game with all of my figures invisible. I uncorked several artillery volleys, decimating tanks on both sides. That triggered some head-scratching on both sides, as the destruction was beyond what the weapons on either side could do. Eventually, some of my forces became visible, and both Human forces turned all of their guns on my forces, grinding my uber-weapons into metallic dust. I did, however, manage to slaughter several infantry units, sneaking along a factory wall, below my Alien infantry, looking down upon them, from second story windows. After dropping stun grenades out of the windows, my infantry ran out and made short work of the stunned, enemy Humans with their light sabers. My Aliens were quickly decimated, and then the Humans resumed their battle against one another.
It was fun, but your more direct take on the Alien forces, without a third faction who might 'switch sides', so to speak, makes it more of a purely SF battle.
This is a classic venue for gaming with Army Men figures. There are plenty of toys out their to use as Bug Aliens, for opposing forces. There are also Transformer figures, in the 4" range, to use as fodder for a game. I will have to go take a 'research trip' to Wal-Mart to check out the possibilities! Cheers!