Neuralyzing hive-minds is considered to be nearly impossible - it is even said that any powerful enough hive-mind discovering the PPC would cause an Emergency. Then again, as it has been already said, QB would probably find the PPC useful.

About getting rid of QB, the plan is simple:

- Kill one with sniper rifle. (PSG-1 or SVD recommended. M82A1 if he is discovered to be resilient to gunfire)
- Wait for another one to teleport in.
- Kill that one too.
- Rinse and repeat.

In the eventuality that QB discovers the plan and a swarm of them starts chasing you, use of rapid-fire shotguns (AA-12, Pancor Jackhammer, Saiga 12) is recommended.
If he turns the Puella Magi against you, knock them out with tranquilizer guns first (M9 from Metal Gear Solid 2 recommended. MGS3's Mosing Nagant if they are distant.)

As Team Fortress 2's Sniper would say, prioritize you targets, be efficient, and have a plan to kill everyone you meet.

After all, darkness accumulates from fighting witches (or possibly from despair, but witches are certainly going to increase that), so letting some of them go all witchy is in his best interests. Or maybe he's just lazy and likes how convenient Grief Seeds are as a despair-concentration mechanism.

Re: the general hive mind neuralyzation issue: I think that'd depend on the being in question. You might have a chance with something like the Zerg or the Vord if you could get to the Queen (since she directly controls them), but I doubt it'd have any effect on any other member of the swarm. Whereas with the Incubators, where all the individual critters seem to be identical, there's no centralized target to go after.

On the plus side, QB would probably be very understanding of PPC agents; after all, Sues degrade reality, which hastens the end of the universe.