This is something I've been thinking a lot about recently but I'm still not sure what is right. My rule of thumb has been that I'll kill any bug that is infesting my house or causing a problem to my health. Like I would kill termites or bed bugs if I had those, or like a leech or a tick. But recently I've been getting a lot of flies in my apartment and while they are technically "infesting" the place, they're not doing anything to harm me, just annoy me. Is it wrong to kill them?
Also I would like to say that if I encountered any of these bugs out in nature I would leave them alone and not harm them, this is only in the context of a threat to your sanitation or home
Indoors: all pests but only pests. They'll take over and get you sick / very unhappy if you don't deal with them thoroughly. Flies included - they tend to cross-contaminate, as they lay eggs on gross things, then land on and eat food you later ingest. If you have a pet that poops indoors, they're gonna create a fecal-oral route, a very common vector for pathogens.
Outdoors: only the ones actively trying to hurt me like hornets, horseflies, etc.