I'd consider using D6 for an Inquisitor game IF you're focused on a small heroic team ala Dark Heresy. I'm ok with the Dark Heresy 1e RPG, but I beat it with a stick until it behaves and I suspect D6 could achieve the same goal.
However, if you're thinking about a Inquisitor retinue that can field serious hardware and loyal troops in skirmish/mass combat, then Savage Worlds works nicely for filling the table with 40k toys. I ran an IG game with the concept the PCs were Big Damn Heroes pulled from various sources - we had an Ultramarine, an Inquisitor, legendary Commissar, IG heroes, etc. and they had an IG company at their disposal.
I'd argue Savage Worlds works better for Necromunda than Necromunda. I've run a couple SW Necromunda one-shots and they were excellent - twice as much violence in half the time. Totally would run that again in a heartbeat. I imagine running Mordheim would have the same result.