Yes, but Lizard is talking about beating the Aliens without their own weapons. I reckon that Incendiary Rockets might work, but you would need to have an ambush set up really well for it to work.
Oh and you can play as the Aliens if you play UFO 2000 which is basically a UFO skirmish game. You 'buy' soldiers and different weapons and it is multi-player.
I don't know what the penalty for ignoring an alien base is, but I bet that it is really high. Nothing you can't make up for by shooting down supply ships, though.
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