Elder Gods in SF are generally quite a pain in the ass. Advanced and nigh inscrutable beings they usually show up at random, announce we are primitive savages and then try to stop a war or otherwise screw up our fun times. Maybe they're trying to teach us some morality. Otherwise it seems as absurd as a human trying to break up a fight between two ant colonies. Maybe it's their equivalent of community service to the Near Eternal Gods.
Elder gods are hard to work into an SF rpg because they are often portrayed as being able to do whatever the heck they want (I'm looking at you Q Continuum!) Even those who have limits are often way above your Captain's pay grade. Maybe the giant glowing head chasing your destroyer is about as powerful as a dreadnought. That still isn't helping. There are some considerations when employing an elder god in a scenario or campaign (good luck).
1) Less is more. Over exposure is a great way to destroy the mystique and menace of these guys. The Organians only played their cards before the last commercial break as opposed to Q who is just too annoying for words. Honestly, I'd shoot him with a phaser on setting ten. It probably wouldn't bother him but it'd make me feel better.
2) Their motives can be incomprehensible to us short lived mortals. Maybe they want to protect a planet of slime molds that will evolve into a beautiful and benevolent culture. Maybe they just want to give the Europans a chance to develop before we start selling them Starbucks franchises (see my Coffee blog post for more on this. Beings that don't have any use for coffee are incomprehensible to me.)
3) They might not be monolithic. A space god might still have to worry about his peers. He might get called home after playing by his angry parents ("... and put the Orion Arm back the way you found it! Sorry humans. ") Your scenario blocker might have to pay a price for intervention or have limits on what can be done before other elder gods show up to ruin the party.
a) You might be lucky enough to be caught between a war of the gods. This can go one of two ways: either the gods of both sides cancel out and need your gang for tie breakers or they don't cancel out and your game master is a real bastard.
4) They aren't that powerful. Your starship crewmen could be gods to the iron age locals but they can still be taken out by a spear or a bacteria for that matter. The natives don't know this but wait till one of your band cuts themselves shaving. So the personification of Cloacina (Roman goddess of sewers!) might be vulnerable to a tac nuke, or enough energy weapon fire or have a finite energy supply or a vulnerable power source. You get the idea.
a) They might be charlatans masquerading as gods. Maybe they just found a ring of power in a pig's nose or an alien's lobe.
5) They have vulnerabilities. Maybe someone created a sword of god slaying (or a robot tank of god slaying). Maybe you have to decoy them to that pre-supernova at just the right time. Perhaps you can trap them in a black hole (minor deities can be trapped on a neutron star.)