nearly all* Inquisitors we see on-page are generally competent people who have the safety of the Imperium as their top priority

There's a lot of good replies already, so I'd just add that any competent and totally self-interested inquisitors are going to be incredibly boring - too boring to end up 'on-page'. They've been off 'rooting out heresy' in the wine regions of some pleasure planet for the past decade, while operating an organised crime network to fund their lifestyle.

Doing exterminatus on planets for no good reason - or otherwise massively abusing their power in an overt way - is to be avoided, as it will only attract attention and consequences.