So you probably can’t shoot the hero. Get over it. We supervillains are supposed to be clever, aren’t we? There are other ways we can make the idiot hero sorry he ever dared to go up against our evil magnificence!
One possibility is to aim for the sidekick. The sidekicks are often the smaller and, frankly, wimpier of any heroic duo, appreciated for his brains instead of his brawn (or other things, if you happen to be fighting a hero of vague sexual persuasion).
The writer is less likely to be protecting the sidekick, because even they can only stretch plausability so far. If you are lucky, the writer may even allow you to kill the sidekick, having been planning his death all along to allow his hero an emotional moment (or several) over his or her fallen friend.
This is especially likely if the sidekick is incredibly annoying - the writer may even be planning for you to kill the sidekick, just to get him the heck out of the way. It’s a good way for them to wallow in angst without killing off anyone they actually need from week to week (this can also apply to love interests, so if there’s a likely candidate in the immediate vicinity you might as well take a test shot).
Even if it isn't the sidekick's time to go to that great tacky costume shop in the sky, there's still a chance you can badly injure him. Since the sidekick's main job is to yell "watch out!" to the hero at inappropriate moments, heavy bleeding will to nothing to deter their mission. If nothing else, you can use it as a distraction while you do something far more interesting with your time.
Note: When planning an attack from space, the supervillain's aiming curse is somehow lessened dramatically, especially in one on one combat between ships. Photon torpedoes tend to have a rather dramatic reaction, especially when fired at a minor hero. In general, it is the only shoot-out situation which can reliably won by a villain.