There are all sorts of ways that games handle their deities. Some assign stats to them as though they were just really powerful characters. I hate that. I’ve read a lot of myths, and I don’t recall Hercules or any of the others killing any gods. Once you assign the amount of damage it takes to kill one, you are just asking the PCs to go and try (and probably succeed).
I’m all for limiting the powers of the divine. I wrote an article on it. (Find it here.) Unable to skew the game towards the player characters = good! Able to be killed = bad! At least in my measure.
So how do you keep them in check? Well, look at that article, I think that lays it out pretty well. If you want your characters to “kill a god”, I think you need to set up the god’s (or whatever) avatar on the world, and let them kill that. That way they have attacked and killed a divine creature, likely ruining his plans, but still they have not actually eliminated a divine creature that should be beyond such silly little things like death. Now if the king of the gods wants to kill a god, well, that’s another story!
I like the myths that treat the gods like they are a dysfunctional royal family with intrigues and enemies outside the pantheon. If one pantheon is in power (either in a region or across the world) I like putting in little upstarts who are looking to steal their piece of the pie without being assaulted by celestial hordes. In one campaign, the “god” of rats wanted to become the god of cities, and set out to diminish his rival’s power until he could usurp his place. In that campaign, there were also some tricks played where lesser spirits were sabotaging some of the gods’ altars in order to redirect the sacrifices to them, directly stealing power, though in truth relatively small pieces of power.
These are the types of power plays that mortal characters can get involved in (intentionally or accidently). Here is where the gods can play a direct part in the campaign, but without all the lightning bolts and thunderous voices.