Acolytes are a very important asset in intelligence gathering and something of a tertiary role of problem solving in small situations, they're what's known as a mk1 eyeball. Otherwise 40k is still a very primitive existance technologically, they don't have streets full of security cameras, easily accessible databases like an internet, phone networks and a somewhat 'silo' job environment where cross-communication with peers isn't always widely adopted.
So in a way, yes the Acolyte is a peon amongst trillions, but he/she is actually critical in getting information back to the boss as well as a different opinion the Inq might not always have outside their inner-circle of professional advisors. Plus, for the acolyte its a 'ladder climb' for them in the Imperium in terms of personal power, influence, cash and career which most of the time locks people into some kind of service from birth to death. They might not necessarily make Inquisitor themselves, but they'll fast track it up the ranks of people that matter...
...course, the problem always the (much higher than average) possibility of being eaten by hostile xenos, soul stolen by daemons, corruption and some underhive scum running around with their head on a stick
Putting a world to the sword so to speak isn't easy either, aside from the polical rammifications it is 'the' very last resort. You have to remember that they might be heretical filth, but they're more than likely sitting on what may well be centuries of critical infrastructure that the Imperium needs to fight its wars, feed people, make machines and so forth. That if it was removed by saturation bombing or cyclonics- might actually affect a much larger sphere of influence that puts an even bigger hole in the Imperium. Worlds that aren't churning out las-guns to baneblades, warp engines to ration packs or even just raising 19million Imperial Guard a year get noticed if they go missing and having half a dozen culties running around is literally not the end of the world.
Half a dozen acolytes that get their arses killed by cultists just means to Mr/Mrs Inquisitor, I need to recruit another 6 acolytes and l have to formulate a much stronger response to the matter now we have a much better idea of the situation.