A few things- do your antagonist NPCs fight smart or just charge blindly? Because let me tell you, even with primitive weapons, a group of three random dregs in a bar is more than enough to pound any acolyte group into the dirt, especially at rank three or below. I know this from personal experience, as until a small brawl in the Barking Saint spilled over into a thousand round ballistic buffet, my party were getting their collective posteriors handed to them on a rather dirty platter. Essentially, have your goons flank, out number, aim and all those sneaky tricks players seem to think are theirs alone to get the best possible bonus, then use called shots, full auto, scatter or whatever to try and beat them. Don't be afraid to gang up. You don't have to kill your group, just make sure it's clear the bad guys have the upper hand. If the NPCs have microbeads, have them keep in constant contact. Talking is a free action,so have them call for support, get their friends to pull the wounded out of there and above all- disengage and retreat in good order when they start losing, and make sure they grab their fallen on the way out. Hell, have the goons loot their own dead in battle for more ammo, grenades, a slightly better weapon, etc.
I also recommend having the Inquisitor give them a working budget- I gave my group 3000 thrones to begin with, plus free bed, board and transit. So far they have only looted three bodies, two of which were plot-related (the third was a loot of opportunity, as they had to search fast and skedaddle before the Magistratum arrived). Admittedly, that looting netted them a bolt pistol, two power blades and a best quality autopistol, plus access to a rather full account with a transtellar merchant banking conglomerate, but the point stands that they've generally avoided looting in favour of maintaining a low profile because they felt they had the funds to keep them sufficiently tooled up and badass (a cleric and a noble in the party probably helps).
I'll also note that they have, in the last session, spent the entirety of their Inquisitorial budget, plus pretty much all of the locally available cash in the Goldenhand account they looted, in order to tool up for a planned covert ops insertion, and pay for an emergency astropathic message to their boss, and so now all have armour-plated stealth underwear...
It is therefore possible that they'll be doing some serious looting later, but given that their next payday is in a couple of Imperial Year Fractions, I slightly doubt it.