Yeah, that's always what bothers me about sci fi wars where no one ever lands troops.
We have nuclear weapons nowadays, and orbital bombardment. For those who don't have those capabilities, we could quite easily say 'Give up or we nuke you'. Maybe it works, maybe they refuse anyway, or we're talking to fanatics, and so on. If it works, alright, whatever, your country is now seen as a dick but you have nukes so who cares, right? I mean, so do those other countries but whatever, we'll just out-nuke them.
But if they don't? Well, you're left with a choice.
Follow through, or back out. You follow through, you've probably lost whatever you were hoping to gain by having that area/those people under your jurisdiction. Exceptions might be if you do a bomb drop here or there and see how long until their imminent deaths get through to their brains and they give up. But you don't need nukes to do that, and precision fire support from space is still a thing. Doing it to civilian centers on purpose? Well...rebuilding industrial centers is usually expensive, and having a very ill-contented people isn't that great an idea. Especially since guerillas are really hard to deal with, short of genocide. In 40k, equivalent of this is Orks, since you need Exterminatus or enough fire to satisfy a Canoness to 'permanently' get rid of them. Imperium's just lucky the populace isn't supporting the orks...
This post has been open for hours now and I've long lost my train of thought. *shrug*