The way I approach it is this: CCP has stated that every player is a roleplayer; some "immersionists" just take the level of immersion deeper than others. That means that, kill for kill, all actions are in-character. This is justified through the notion of the populated solar system.
Caveat: the number of missions is finite. The scope of human experience (professional or otherwise) is not. I'll get to that.
Now, it is only believable that mission runners get the level of business, and the scale of conflict (read: body count), if, and only if, virtually every system in the game, from 1.0 to 0.0, is constantly in what we would regard as a state of high-level warfare, involving massive fleets of battleships and facilities. Don't think late-continuity "Star Trek: DS9" -style battles; think more along the lines of several-thousand-battleship fleets from essentially every faction operating out of numerous hidey-holes in essentially every system, essentially all at once.
The fiction seems to support this understanding. Consider that mid-sized battleship fleets will be referred to at times as scouting elements.
One way to justify this is to think of these fleets as spending most of their time in standoff mode. Pirate fleets conduct raids and scouting exercises in force. Navy elements conduct defensive maneuvers similarly, defending a large spacebourne population resident in mining habitats, supply depots, and similar stationary civilian structures that capsuleers rarely get to see. Most of the time, the overall status quo is a sort of a tense stalemate.
It's when and where that changes (and it does, constantly, all over) that capsuleers get tapped. They're troubleshooters for a populated solar system the size of, well, a solar system.
http://www.bbc.com/future/bespoke/space_infographicNew Eden's population has had centuries of interstellar development to spread out into that-- thousands of times that-- and has done so. Assembling a battleship is like putting up a fair-sized office building, but the facilities are busy, busy, busy and a fleet of a thousand office buildings isn't so much to ask when you've got a hundred thousand mid-to-large-size asteroid colonies out there in that one interplanetary asteroid belt (analogous to the one between Mars and Jupiter) all churning away-- and even more working out of the oort cloud. Remember also that these factory-stations are not building to capsuleer design specs.
That's in ONE system. For a major interstellar faction, in this scenario, losing a few battleships is like having a few skin cells flake off.
Does this make capsuleers statistical nonentities, trying to erode away the great mountain of humanity with a garden hose, a few atoms at a time? Not quite.
It is suggested in the fiction that, among the pirate-faction rank and file, the sheer lethality of a capsuleer is little-known. Their leadership knows better. See "Summer Breeze," for a commander's-eye view. Elsewhere, or perhaps just "later" in time, the "Empyreans" are known as "gods of destruction," and the death toll they claim is viewed with ever-growing horror.
Capsuleers are rare; most spacers have never seen one. As populous as they may be around Jita 4-4, they mostly stick to their own dedicated hubs and transit routes, or to designated mission sites (or pirate facilities that didn't stay quiet enough, through probing). Conventional craft steer clear.
(Don't ask me to justify the damned asteroid patrols. I'd need another week with that alone.)
Bottom line: as lethal as they are, capsuleers are less a cluster-depopulating plague and more a strategic tool. They're not cleansing the cluster of human life just yet, but could become demographically significant if there were, say, a hundred times as many of them.
Mind you, the murder rate of your city doesn't have to be actually driving your population downward before you notice it's become a significant problem.
OKAY! ... So, with all that setup, how I approach missions:
They're all real. Except ... they're not exactly as described. No, I haven't rescued that many damsels-- but I might well have been sent on retrieval missions for a variety of abducted personnel. No, I haven't killed The Thief that many times, and he hasn't had pet drones every time, but I've retrieved my share of stolen documents from various inventive persons. The plot provides a rough outline of the "reality" behind the mission, and I look on yet another run of When Worlds Collide in much the same way as I do, real-world, to being handed yet another typical case: ho-hum; another one of these.
The background differs. The faces differ. The specifics differ-- and differ enough to matter. But it's still the same "type" of job.
This absolutely means that if a mission calls for killing civilians, and you take it, you, IC, took a job that involved killing civilians.
/braindump