It really depends on the "power level" of the setting, if the PCs get to a point where they're way stronger than the local government, then, yeah, they might as well just kill everyone who's antagonistic to them. It's about what you'd expect would happen in a world full of superpowered people, really.
If it's a very strong setting overall, something like the Forgotten Realms with several archmages, high-level martials, maybe a few demigods just sitting around in the city, then they can't go too crazy even at high-levels. But in a very high-magic setting you really gotta figure out how they deal with all those things that'd make politics hell, like illusions, mind control, memory changing, shapechangers, resurrection, scrying, wildshape, invoking the power of the gods, etc.
To make the PCs care for what's happening, maybe give them a patron who's involved with all the stuff happening, someone influential that can give them shelter and boons. They get to like this person who's helping them so much, and in return they can be asked to do tasks related to whatever political machinations are happening. Said person can also persuade them against going postal on their enemies, "change the system from within" and all that.
